diff --git a/api/commands.py b/api/commands.py
index 2bef83b2a7..1858cb2734 100644
--- a/api/commands.py
+++ b/api/commands.py
@@ -212,7 +212,9 @@ def migrate_annotation_vector_database():
                 if not dataset_collection_binding:
                     click.echo(f"App annotation collection binding not found: {app.id}")
                     continue
-                annotations = db.session.query(MessageAnnotation).where(MessageAnnotation.app_id == app.id).all()
+                annotations = db.session.scalars(
+                    select(MessageAnnotation).where(MessageAnnotation.app_id == app.id)
+                ).all()
                 dataset = Dataset(
                     id=app.id,
                     tenant_id=app.tenant_id,
@@ -367,29 +369,25 @@ def migrate_knowledge_vector_database():
                     )
                     raise e
 
-                dataset_documents = (
-                    db.session.query(DatasetDocument)
-                    .where(
+                dataset_documents = db.session.scalars(
+                    select(DatasetDocument).where(
                         DatasetDocument.dataset_id == dataset.id,
                         DatasetDocument.indexing_status == "completed",
                         DatasetDocument.enabled == True,
                         DatasetDocument.archived == False,
                     )
-                    .all()
-                )
+                ).all()
 
                 documents = []
                 segments_count = 0
                 for dataset_document in dataset_documents:
-                    segments = (
-                        db.session.query(DocumentSegment)
-                        .where(
+                    segments = db.session.scalars(
+                        select(DocumentSegment).where(
                             DocumentSegment.document_id == dataset_document.id,
                             DocumentSegment.status == "completed",
                             DocumentSegment.enabled == True,
                         )
-                        .all()
-                    )
+                    ).all()
 
                     for segment in segments:
                         document = Document(
diff --git a/api/controllers/console/apikey.py b/api/controllers/console/apikey.py
index 06de2fa6b6..56c61c2886 100644
--- a/api/controllers/console/apikey.py
+++ b/api/controllers/console/apikey.py
@@ -60,11 +60,11 @@ class BaseApiKeyListResource(Resource):
         assert self.resource_id_field is not None, "resource_id_field must be set"
         resource_id = str(resource_id)
         _get_resource(resource_id, current_user.current_tenant_id, self.resource_model)
-        keys = (
-            db.session.query(ApiToken)
-            .where(ApiToken.type == self.resource_type, getattr(ApiToken, self.resource_id_field) == resource_id)
-            .all()
-        )
+        keys = db.session.scalars(
+            select(ApiToken).where(
+                ApiToken.type == self.resource_type, getattr(ApiToken, self.resource_id_field) == resource_id
+            )
+        ).all()
         return {"items": keys}
 
     @marshal_with(api_key_fields)
diff --git a/api/controllers/console/datasets/data_source.py b/api/controllers/console/datasets/data_source.py
index 45c647659b..6e49bfa510 100644
--- a/api/controllers/console/datasets/data_source.py
+++ b/api/controllers/console/datasets/data_source.py
@@ -29,14 +29,12 @@ class DataSourceApi(Resource):
     @marshal_with(integrate_list_fields)
     def get(self):
         # get workspace data source integrates
-        data_source_integrates = (
-            db.session.query(DataSourceOauthBinding)
-            .where(
+        data_source_integrates = db.session.scalars(
+            select(DataSourceOauthBinding).where(
                 DataSourceOauthBinding.tenant_id == current_user.current_tenant_id,
                 DataSourceOauthBinding.disabled == False,
             )
-            .all()
-        )
+        ).all()
 
         base_url = request.url_root.rstrip("/")
         data_source_oauth_base_path = "/console/api/oauth/data-source"
diff --git a/api/controllers/console/datasets/datasets.py b/api/controllers/console/datasets/datasets.py
index 11b7b1fec0..9fb092607a 100644
--- a/api/controllers/console/datasets/datasets.py
+++ b/api/controllers/console/datasets/datasets.py
@@ -2,6 +2,7 @@ import flask_restx
 from flask import request
 from flask_login import current_user
 from flask_restx import Resource, marshal, marshal_with, reqparse
+from sqlalchemy import select
 from werkzeug.exceptions import Forbidden, NotFound
 
 import services
@@ -411,11 +412,11 @@ class DatasetIndexingEstimateApi(Resource):
         extract_settings = []
         if args["info_list"]["data_source_type"] == "upload_file":
             file_ids = args["info_list"]["file_info_list"]["file_ids"]
-            file_details = (
-                db.session.query(UploadFile)
-                .where(UploadFile.tenant_id == current_user.current_tenant_id, UploadFile.id.in_(file_ids))
-                .all()
-            )
+            file_details = db.session.scalars(
+                select(UploadFile).where(
+                    UploadFile.tenant_id == current_user.current_tenant_id, UploadFile.id.in_(file_ids)
+                )
+            ).all()
 
             if file_details is None:
                 raise NotFound("File not found.")
@@ -518,11 +519,11 @@ class DatasetIndexingStatusApi(Resource):
     @account_initialization_required
     def get(self, dataset_id):
         dataset_id = str(dataset_id)
-        documents = (
-            db.session.query(Document)
-            .where(Document.dataset_id == dataset_id, Document.tenant_id == current_user.current_tenant_id)
-            .all()
-        )
+        documents = db.session.scalars(
+            select(Document).where(
+                Document.dataset_id == dataset_id, Document.tenant_id == current_user.current_tenant_id
+            )
+        ).all()
         documents_status = []
         for document in documents:
             completed_segments = (
@@ -569,11 +570,11 @@ class DatasetApiKeyApi(Resource):
     @account_initialization_required
     @marshal_with(api_key_list)
     def get(self):
-        keys = (
-            db.session.query(ApiToken)
-            .where(ApiToken.type == self.resource_type, ApiToken.tenant_id == current_user.current_tenant_id)
-            .all()
-        )
+        keys = db.session.scalars(
+            select(ApiToken).where(
+                ApiToken.type == self.resource_type, ApiToken.tenant_id == current_user.current_tenant_id
+            )
+        ).all()
         return {"items": keys}
 
     @setup_required
diff --git a/api/controllers/console/datasets/datasets_document.py b/api/controllers/console/datasets/datasets_document.py
index c9c0b6a5ce..f943fb3ccb 100644
--- a/api/controllers/console/datasets/datasets_document.py
+++ b/api/controllers/console/datasets/datasets_document.py
@@ -1,5 +1,6 @@
 import logging
 from argparse import ArgumentTypeError
+from collections.abc import Sequence
 from typing import Literal, cast
 
 from flask import request
@@ -79,7 +80,7 @@ class DocumentResource(Resource):
 
         return document
 
-    def get_batch_documents(self, dataset_id: str, batch: str) -> list[Document]:
+    def get_batch_documents(self, dataset_id: str, batch: str) -> Sequence[Document]:
         dataset = DatasetService.get_dataset(dataset_id)
         if not dataset:
             raise NotFound("Dataset not found.")
diff --git a/api/controllers/console/explore/installed_app.py b/api/controllers/console/explore/installed_app.py
index 22aa753d92..bdc3fb0dbd 100644
--- a/api/controllers/console/explore/installed_app.py
+++ b/api/controllers/console/explore/installed_app.py
@@ -3,7 +3,7 @@ from typing import Any
 
 from flask import request
 from flask_restx import Resource, inputs, marshal_with, reqparse
-from sqlalchemy import and_
+from sqlalchemy import and_, select
 from werkzeug.exceptions import BadRequest, Forbidden, NotFound
 
 from controllers.console import api
@@ -33,13 +33,15 @@ class InstalledAppsListApi(Resource):
         current_tenant_id = current_user.current_tenant_id
 
         if app_id:
-            installed_apps = (
-                db.session.query(InstalledApp)
-                .where(and_(InstalledApp.tenant_id == current_tenant_id, InstalledApp.app_id == app_id))
-                .all()
-            )
+            installed_apps = db.session.scalars(
+                select(InstalledApp).where(
+                    and_(InstalledApp.tenant_id == current_tenant_id, InstalledApp.app_id == app_id)
+                )
+            ).all()
         else:
-            installed_apps = db.session.query(InstalledApp).where(InstalledApp.tenant_id == current_tenant_id).all()
+            installed_apps = db.session.scalars(
+                select(InstalledApp).where(InstalledApp.tenant_id == current_tenant_id)
+            ).all()
 
         if current_user.current_tenant is None:
             raise ValueError("current_user.current_tenant must not be None")
diff --git a/api/controllers/console/workspace/account.py b/api/controllers/console/workspace/account.py
index bd078729c4..7a41a8a5cc 100644
--- a/api/controllers/console/workspace/account.py
+++ b/api/controllers/console/workspace/account.py
@@ -248,7 +248,9 @@ class AccountIntegrateApi(Resource):
             raise ValueError("Invalid user account")
         account = current_user
 
-        account_integrates = db.session.query(AccountIntegrate).where(AccountIntegrate.account_id == account.id).all()
+        account_integrates = db.session.scalars(
+            select(AccountIntegrate).where(AccountIntegrate.account_id == account.id)
+        ).all()
 
         base_url = request.url_root.rstrip("/")
         oauth_base_path = "/console/api/oauth/login"
diff --git a/api/core/memory/token_buffer_memory.py b/api/core/memory/token_buffer_memory.py
index 7be695812a..1f2525cfed 100644
--- a/api/core/memory/token_buffer_memory.py
+++ b/api/core/memory/token_buffer_memory.py
@@ -32,11 +32,16 @@ class TokenBufferMemory:
         self.model_instance = model_instance
 
     def _build_prompt_message_with_files(
-        self, message_files: list[MessageFile], text_content: str, message: Message, app_record, is_user_message: bool
+        self,
+        message_files: Sequence[MessageFile],
+        text_content: str,
+        message: Message,
+        app_record,
+        is_user_message: bool,
     ) -> PromptMessage:
         """
         Build prompt message with files.
-        :param message_files: list of MessageFile objects
+        :param message_files: Sequence of MessageFile objects
         :param text_content: text content of the message
         :param message: Message object
         :param app_record: app record
@@ -128,14 +133,12 @@ class TokenBufferMemory:
         prompt_messages: list[PromptMessage] = []
         for message in messages:
             # Process user message with files
-            user_files = (
-                db.session.query(MessageFile)
-                .where(
+            user_files = db.session.scalars(
+                select(MessageFile).where(
                     MessageFile.message_id == message.id,
                     (MessageFile.belongs_to == "user") | (MessageFile.belongs_to.is_(None)),
                 )
-                .all()
-            )
+            ).all()
 
             if user_files:
                 user_prompt_message = self._build_prompt_message_with_files(
@@ -150,11 +153,9 @@ class TokenBufferMemory:
                 prompt_messages.append(UserPromptMessage(content=message.query))
 
             # Process assistant message with files
-            assistant_files = (
-                db.session.query(MessageFile)
-                .where(MessageFile.message_id == message.id, MessageFile.belongs_to == "assistant")
-                .all()
-            )
+            assistant_files = db.session.scalars(
+                select(MessageFile).where(MessageFile.message_id == message.id, MessageFile.belongs_to == "assistant")
+            ).all()
 
             if assistant_files:
                 assistant_prompt_message = self._build_prompt_message_with_files(
diff --git a/api/core/ops/arize_phoenix_trace/arize_phoenix_trace.py b/api/core/ops/arize_phoenix_trace/arize_phoenix_trace.py
index e7c90c1229..c5fbe4d78b 100644
--- a/api/core/ops/arize_phoenix_trace/arize_phoenix_trace.py
+++ b/api/core/ops/arize_phoenix_trace/arize_phoenix_trace.py
@@ -15,6 +15,7 @@ from opentelemetry.sdk.resources import Resource
 from opentelemetry.sdk.trace.export import SimpleSpanProcessor
 from opentelemetry.sdk.trace.id_generator import RandomIdGenerator
 from opentelemetry.trace import SpanContext, TraceFlags, TraceState
+from sqlalchemy import select
 
 from core.ops.base_trace_instance import BaseTraceInstance
 from core.ops.entities.config_entity import ArizeConfig, PhoenixConfig
@@ -699,8 +700,8 @@ class ArizePhoenixDataTrace(BaseTraceInstance):
 
     def _get_workflow_nodes(self, workflow_run_id: str):
         """Helper method to get workflow nodes"""
-        workflow_nodes = (
-            db.session.query(
+        workflow_nodes = db.session.scalars(
+            select(
                 WorkflowNodeExecutionModel.id,
                 WorkflowNodeExecutionModel.tenant_id,
                 WorkflowNodeExecutionModel.app_id,
@@ -713,10 +714,8 @@ class ArizePhoenixDataTrace(BaseTraceInstance):
                 WorkflowNodeExecutionModel.elapsed_time,
                 WorkflowNodeExecutionModel.process_data,
                 WorkflowNodeExecutionModel.execution_metadata,
-            )
-            .where(WorkflowNodeExecutionModel.workflow_run_id == workflow_run_id)
-            .all()
-        )
+            ).where(WorkflowNodeExecutionModel.workflow_run_id == workflow_run_id)
+        ).all()
         return workflow_nodes
 
     def _construct_llm_attributes(self, prompts: dict | list | str | None) -> dict[str, str]:
diff --git a/api/core/rag/datasource/vdb/tidb_on_qdrant/tidb_service.py b/api/core/rag/datasource/vdb/tidb_on_qdrant/tidb_service.py
index 184b5f2142..e1d4422144 100644
--- a/api/core/rag/datasource/vdb/tidb_on_qdrant/tidb_service.py
+++ b/api/core/rag/datasource/vdb/tidb_on_qdrant/tidb_service.py
@@ -1,5 +1,6 @@
 import time
 import uuid
+from collections.abc import Sequence
 
 import requests
 from requests.auth import HTTPDigestAuth
@@ -139,7 +140,7 @@ class TidbService:
 
     @staticmethod
     def batch_update_tidb_serverless_cluster_status(
-        tidb_serverless_list: list[TidbAuthBinding],
+        tidb_serverless_list: Sequence[TidbAuthBinding],
         project_id: str,
         api_url: str,
         iam_url: str,
diff --git a/api/core/tools/custom_tool/provider.py b/api/core/tools/custom_tool/provider.py
index 5790aea2b0..0cc992155a 100644
--- a/api/core/tools/custom_tool/provider.py
+++ b/api/core/tools/custom_tool/provider.py
@@ -1,4 +1,5 @@
 from pydantic import Field
+from sqlalchemy import select
 
 from core.entities.provider_entities import ProviderConfig
 from core.tools.__base.tool_provider import ToolProviderController
@@ -176,11 +177,11 @@ class ApiToolProviderController(ToolProviderController):
         tools: list[ApiTool] = []
 
         # get tenant api providers
-        db_providers: list[ApiToolProvider] = (
-            db.session.query(ApiToolProvider)
-            .where(ApiToolProvider.tenant_id == tenant_id, ApiToolProvider.name == self.entity.identity.name)
-            .all()
-        )
+        db_providers = db.session.scalars(
+            select(ApiToolProvider).where(
+                ApiToolProvider.tenant_id == tenant_id, ApiToolProvider.name == self.entity.identity.name
+            )
+        ).all()
 
         if db_providers and len(db_providers) != 0:
             for db_provider in db_providers:
diff --git a/api/core/tools/tool_label_manager.py b/api/core/tools/tool_label_manager.py
index 84b874975a..39646b7fc8 100644
--- a/api/core/tools/tool_label_manager.py
+++ b/api/core/tools/tool_label_manager.py
@@ -87,9 +87,7 @@ class ToolLabelManager:
             assert isinstance(controller, ApiToolProviderController | WorkflowToolProviderController)
             provider_ids.append(controller.provider_id)  # ty: ignore [unresolved-attribute]
 
-        labels: list[ToolLabelBinding] = (
-            db.session.query(ToolLabelBinding).where(ToolLabelBinding.tool_id.in_(provider_ids)).all()
-        )
+        labels = db.session.scalars(select(ToolLabelBinding).where(ToolLabelBinding.tool_id.in_(provider_ids))).all()
 
         tool_labels: dict[str, list[str]] = {label.tool_id: [] for label in labels}
 
diff --git a/api/core/tools/tool_manager.py b/api/core/tools/tool_manager.py
index bc1f09a2fc..b29da3f0ba 100644
--- a/api/core/tools/tool_manager.py
+++ b/api/core/tools/tool_manager.py
@@ -667,9 +667,9 @@ class ToolManager:
 
             # get db api providers
             if "api" in filters:
-                db_api_providers: list[ApiToolProvider] = (
-                    db.session.query(ApiToolProvider).where(ApiToolProvider.tenant_id == tenant_id).all()
-                )
+                db_api_providers = db.session.scalars(
+                    select(ApiToolProvider).where(ApiToolProvider.tenant_id == tenant_id)
+                ).all()
 
                 api_provider_controllers: list[dict[str, Any]] = [
                     {"provider": provider, "controller": ToolTransformService.api_provider_to_controller(provider)}
@@ -690,9 +690,9 @@ class ToolManager:
 
             if "workflow" in filters:
                 # get workflow providers
-                workflow_providers: list[WorkflowToolProvider] = (
-                    db.session.query(WorkflowToolProvider).where(WorkflowToolProvider.tenant_id == tenant_id).all()
-                )
+                workflow_providers = db.session.scalars(
+                    select(WorkflowToolProvider).where(WorkflowToolProvider.tenant_id == tenant_id)
+                ).all()
 
                 workflow_provider_controllers: list[WorkflowToolProviderController] = []
                 for workflow_provider in workflow_providers:
diff --git a/api/events/event_handlers/update_app_dataset_join_when_app_model_config_updated.py b/api/events/event_handlers/update_app_dataset_join_when_app_model_config_updated.py
index b8b5a89dc5..69959acd19 100644
--- a/api/events/event_handlers/update_app_dataset_join_when_app_model_config_updated.py
+++ b/api/events/event_handlers/update_app_dataset_join_when_app_model_config_updated.py
@@ -1,3 +1,5 @@
+from sqlalchemy import select
+
 from events.app_event import app_model_config_was_updated
 from extensions.ext_database import db
 from models.dataset import AppDatasetJoin
@@ -13,7 +15,7 @@ def handle(sender, **kwargs):
 
     dataset_ids = get_dataset_ids_from_model_config(app_model_config)
 
-    app_dataset_joins = db.session.query(AppDatasetJoin).where(AppDatasetJoin.app_id == app.id).all()
+    app_dataset_joins = db.session.scalars(select(AppDatasetJoin).where(AppDatasetJoin.app_id == app.id)).all()
 
     removed_dataset_ids: set[str] = set()
     if not app_dataset_joins:
diff --git a/api/events/event_handlers/update_app_dataset_join_when_app_published_workflow_updated.py b/api/events/event_handlers/update_app_dataset_join_when_app_published_workflow_updated.py
index fcc3b63fa7..898ec1f153 100644
--- a/api/events/event_handlers/update_app_dataset_join_when_app_published_workflow_updated.py
+++ b/api/events/event_handlers/update_app_dataset_join_when_app_published_workflow_updated.py
@@ -1,5 +1,7 @@
 from typing import cast
 
+from sqlalchemy import select
+
 from core.workflow.nodes import NodeType
 from core.workflow.nodes.knowledge_retrieval.entities import KnowledgeRetrievalNodeData
 from events.app_event import app_published_workflow_was_updated
@@ -15,7 +17,7 @@ def handle(sender, **kwargs):
     published_workflow = cast(Workflow, published_workflow)
 
     dataset_ids = get_dataset_ids_from_workflow(published_workflow)
-    app_dataset_joins = db.session.query(AppDatasetJoin).where(AppDatasetJoin.app_id == app.id).all()
+    app_dataset_joins = db.session.scalars(select(AppDatasetJoin).where(AppDatasetJoin.app_id == app.id)).all()
 
     removed_dataset_ids: set[str] = set()
     if not app_dataset_joins:
diff --git a/api/models/account.py b/api/models/account.py
index 019159d2da..4656b47e7a 100644
--- a/api/models/account.py
+++ b/api/models/account.py
@@ -218,10 +218,12 @@ class Tenant(Base):
     updated_at: Mapped[datetime] = mapped_column(DateTime, server_default=func.current_timestamp())
 
     def get_accounts(self) -> list[Account]:
-        return (
-            db.session.query(Account)
-            .where(Account.id == TenantAccountJoin.account_id, TenantAccountJoin.tenant_id == self.id)
-            .all()
+        return list(
+            db.session.scalars(
+                select(Account).where(
+                    Account.id == TenantAccountJoin.account_id, TenantAccountJoin.tenant_id == self.id
+                )
+            ).all()
         )
 
     @property
diff --git a/api/models/dataset.py b/api/models/dataset.py
index 07f3eb18db..13087bf995 100644
--- a/api/models/dataset.py
+++ b/api/models/dataset.py
@@ -208,7 +208,9 @@ class Dataset(Base):
 
     @property
     def doc_metadata(self):
-        dataset_metadatas = db.session.query(DatasetMetadata).where(DatasetMetadata.dataset_id == self.id).all()
+        dataset_metadatas = db.session.scalars(
+            select(DatasetMetadata).where(DatasetMetadata.dataset_id == self.id)
+        ).all()
 
         doc_metadata = [
             {
@@ -1055,13 +1057,11 @@ class ExternalKnowledgeApis(Base):
 
     @property
     def dataset_bindings(self) -> list[dict[str, Any]]:
-        external_knowledge_bindings = (
-            db.session.query(ExternalKnowledgeBindings)
-            .where(ExternalKnowledgeBindings.external_knowledge_api_id == self.id)
-            .all()
-        )
+        external_knowledge_bindings = db.session.scalars(
+            select(ExternalKnowledgeBindings).where(ExternalKnowledgeBindings.external_knowledge_api_id == self.id)
+        ).all()
         dataset_ids = [binding.dataset_id for binding in external_knowledge_bindings]
-        datasets = db.session.query(Dataset).where(Dataset.id.in_(dataset_ids)).all()
+        datasets = db.session.scalars(select(Dataset).where(Dataset.id.in_(dataset_ids))).all()
         dataset_bindings: list[dict[str, Any]] = []
         for dataset in datasets:
             dataset_bindings.append({"id": dataset.id, "name": dataset.name})
diff --git a/api/models/model.py b/api/models/model.py
index f8ead1f872..5a4c5de6e1 100644
--- a/api/models/model.py
+++ b/api/models/model.py
@@ -812,7 +812,7 @@ class Conversation(Base):
 
     @property
     def status_count(self):
-        messages = db.session.query(Message).where(Message.conversation_id == self.id).all()
+        messages = db.session.scalars(select(Message).where(Message.conversation_id == self.id)).all()
         status_counts = {
             WorkflowExecutionStatus.RUNNING: 0,
             WorkflowExecutionStatus.SUCCEEDED: 0,
@@ -1090,7 +1090,7 @@ class Message(Base):
 
     @property
     def feedbacks(self):
-        feedbacks = db.session.query(MessageFeedback).where(MessageFeedback.message_id == self.id).all()
+        feedbacks = db.session.scalars(select(MessageFeedback).where(MessageFeedback.message_id == self.id)).all()
         return feedbacks
 
     @property
@@ -1145,7 +1145,7 @@ class Message(Base):
     def message_files(self) -> list[dict[str, Any]]:
         from factories import file_factory
 
-        message_files = db.session.query(MessageFile).where(MessageFile.message_id == self.id).all()
+        message_files = db.session.scalars(select(MessageFile).where(MessageFile.message_id == self.id)).all()
         current_app = db.session.query(App).where(App.id == self.app_id).first()
         if not current_app:
             raise ValueError(f"App {self.app_id} not found")
diff --git a/api/schedule/clean_unused_datasets_task.py b/api/schedule/clean_unused_datasets_task.py
index 63e6132b6a..2b1e6b47cc 100644
--- a/api/schedule/clean_unused_datasets_task.py
+++ b/api/schedule/clean_unused_datasets_task.py
@@ -96,11 +96,11 @@ def clean_unused_datasets_task():
                 break
 
             for dataset in datasets:
-                dataset_query = (
-                    db.session.query(DatasetQuery)
-                    .where(DatasetQuery.created_at > clean_day, DatasetQuery.dataset_id == dataset.id)
-                    .all()
-                )
+                dataset_query = db.session.scalars(
+                    select(DatasetQuery).where(
+                        DatasetQuery.created_at > clean_day, DatasetQuery.dataset_id == dataset.id
+                    )
+                ).all()
 
                 if not dataset_query or len(dataset_query) == 0:
                     try:
@@ -121,15 +121,13 @@ def clean_unused_datasets_task():
                         if should_clean:
                             # Add auto disable log if required
                             if add_logs:
-                                documents = (
-                                    db.session.query(Document)
-                                    .where(
+                                documents = db.session.scalars(
+                                    select(Document).where(
                                         Document.dataset_id == dataset.id,
                                         Document.enabled == True,
                                         Document.archived == False,
                                     )
-                                    .all()
-                                )
+                                ).all()
                                 for document in documents:
                                     dataset_auto_disable_log = DatasetAutoDisableLog(
                                         tenant_id=dataset.tenant_id,
diff --git a/api/schedule/mail_clean_document_notify_task.py b/api/schedule/mail_clean_document_notify_task.py
index 9e32ecc716..ef6edd6709 100644
--- a/api/schedule/mail_clean_document_notify_task.py
+++ b/api/schedule/mail_clean_document_notify_task.py
@@ -3,6 +3,7 @@ import time
 from collections import defaultdict
 
 import click
+from sqlalchemy import select
 
 import app
 from configs import dify_config
@@ -31,9 +32,9 @@ def mail_clean_document_notify_task():
 
     # send document clean notify mail
     try:
-        dataset_auto_disable_logs = (
-            db.session.query(DatasetAutoDisableLog).where(DatasetAutoDisableLog.notified == False).all()
-        )
+        dataset_auto_disable_logs = db.session.scalars(
+            select(DatasetAutoDisableLog).where(DatasetAutoDisableLog.notified == False)
+        ).all()
         # group by tenant_id
         dataset_auto_disable_logs_map: dict[str, list[DatasetAutoDisableLog]] = defaultdict(list)
         for dataset_auto_disable_log in dataset_auto_disable_logs:
diff --git a/api/schedule/update_tidb_serverless_status_task.py b/api/schedule/update_tidb_serverless_status_task.py
index 1bfeb869e2..1befa0e8b5 100644
--- a/api/schedule/update_tidb_serverless_status_task.py
+++ b/api/schedule/update_tidb_serverless_status_task.py
@@ -1,6 +1,8 @@
 import time
+from collections.abc import Sequence
 
 import click
+from sqlalchemy import select
 
 import app
 from configs import dify_config
@@ -15,11 +17,9 @@ def update_tidb_serverless_status_task():
     start_at = time.perf_counter()
     try:
         # check the number of idle tidb serverless
-        tidb_serverless_list = (
-            db.session.query(TidbAuthBinding)
-            .where(TidbAuthBinding.active == False, TidbAuthBinding.status == "CREATING")
-            .all()
-        )
+        tidb_serverless_list = db.session.scalars(
+            select(TidbAuthBinding).where(TidbAuthBinding.active == False, TidbAuthBinding.status == "CREATING")
+        ).all()
         if len(tidb_serverless_list) == 0:
             return
         # update tidb serverless status
@@ -32,7 +32,7 @@ def update_tidb_serverless_status_task():
     click.echo(click.style(f"Update tidb serverless status task success latency: {end_at - start_at}", fg="green"))
 
 
-def update_clusters(tidb_serverless_list: list[TidbAuthBinding]):
+def update_clusters(tidb_serverless_list: Sequence[TidbAuthBinding]):
     try:
         # batch 20
         for i in range(0, len(tidb_serverless_list), 20):
diff --git a/api/services/annotation_service.py b/api/services/annotation_service.py
index 82b1d21179..34681ba111 100644
--- a/api/services/annotation_service.py
+++ b/api/services/annotation_service.py
@@ -263,11 +263,9 @@ class AppAnnotationService:
 
         db.session.delete(annotation)
 
-        annotation_hit_histories = (
-            db.session.query(AppAnnotationHitHistory)
-            .where(AppAnnotationHitHistory.annotation_id == annotation_id)
-            .all()
-        )
+        annotation_hit_histories = db.session.scalars(
+            select(AppAnnotationHitHistory).where(AppAnnotationHitHistory.annotation_id == annotation_id)
+        ).all()
         if annotation_hit_histories:
             for annotation_hit_history in annotation_hit_histories:
                 db.session.delete(annotation_hit_history)
diff --git a/api/services/auth/api_key_auth_service.py b/api/services/auth/api_key_auth_service.py
index f6e960b413..055cf65816 100644
--- a/api/services/auth/api_key_auth_service.py
+++ b/api/services/auth/api_key_auth_service.py
@@ -1,5 +1,7 @@
 import json
 
+from sqlalchemy import select
+
 from core.helper import encrypter
 from extensions.ext_database import db
 from models.source import DataSourceApiKeyAuthBinding
@@ -9,11 +11,11 @@ from services.auth.api_key_auth_factory import ApiKeyAuthFactory
 class ApiKeyAuthService:
     @staticmethod
     def get_provider_auth_list(tenant_id: str):
-        data_source_api_key_bindings = (
-            db.session.query(DataSourceApiKeyAuthBinding)
-            .where(DataSourceApiKeyAuthBinding.tenant_id == tenant_id, DataSourceApiKeyAuthBinding.disabled.is_(False))
-            .all()
-        )
+        data_source_api_key_bindings = db.session.scalars(
+            select(DataSourceApiKeyAuthBinding).where(
+                DataSourceApiKeyAuthBinding.tenant_id == tenant_id, DataSourceApiKeyAuthBinding.disabled.is_(False)
+            )
+        ).all()
         return data_source_api_key_bindings
 
     @staticmethod
diff --git a/api/services/clear_free_plan_tenant_expired_logs.py b/api/services/clear_free_plan_tenant_expired_logs.py
index 3b4cb1900a..f8f89d7428 100644
--- a/api/services/clear_free_plan_tenant_expired_logs.py
+++ b/api/services/clear_free_plan_tenant_expired_logs.py
@@ -6,6 +6,7 @@ from concurrent.futures import ThreadPoolExecutor
 
 import click
 from flask import Flask, current_app
+from sqlalchemy import select
 from sqlalchemy.orm import Session, sessionmaker
 
 from configs import dify_config
@@ -115,7 +116,7 @@ class ClearFreePlanTenantExpiredLogs:
     @classmethod
     def process_tenant(cls, flask_app: Flask, tenant_id: str, days: int, batch: int):
         with flask_app.app_context():
-            apps = db.session.query(App).where(App.tenant_id == tenant_id).all()
+            apps = db.session.scalars(select(App).where(App.tenant_id == tenant_id)).all()
             app_ids = [app.id for app in apps]
             while True:
                 with Session(db.engine).no_autoflush as session:
diff --git a/api/services/dataset_service.py b/api/services/dataset_service.py
index 20a9c73f08..47bd06a7cc 100644
--- a/api/services/dataset_service.py
+++ b/api/services/dataset_service.py
@@ -6,6 +6,7 @@ import secrets
 import time
 import uuid
 from collections import Counter
+from collections.abc import Sequence
 from typing import Any, Literal, Optional
 
 import sqlalchemy as sa
@@ -741,14 +742,12 @@ class DatasetService:
             }
         # get recent 30 days auto disable logs
         start_date = datetime.datetime.now() - datetime.timedelta(days=30)
-        dataset_auto_disable_logs = (
-            db.session.query(DatasetAutoDisableLog)
-            .where(
+        dataset_auto_disable_logs = db.session.scalars(
+            select(DatasetAutoDisableLog).where(
                 DatasetAutoDisableLog.dataset_id == dataset_id,
                 DatasetAutoDisableLog.created_at >= start_date,
             )
-            .all()
-        )
+        ).all()
         if dataset_auto_disable_logs:
             return {
                 "document_ids": [log.document_id for log in dataset_auto_disable_logs],
@@ -885,69 +884,58 @@ class DocumentService:
         return document
 
     @staticmethod
-    def get_document_by_ids(document_ids: list[str]) -> list[Document]:
-        documents = (
-            db.session.query(Document)
-            .where(
+    def get_document_by_ids(document_ids: list[str]) -> Sequence[Document]:
+        documents = db.session.scalars(
+            select(Document).where(
                 Document.id.in_(document_ids),
                 Document.enabled == True,
                 Document.indexing_status == "completed",
                 Document.archived == False,
             )
-            .all()
-        )
+        ).all()
         return documents
 
     @staticmethod
-    def get_document_by_dataset_id(dataset_id: str) -> list[Document]:
-        documents = (
-            db.session.query(Document)
-            .where(
+    def get_document_by_dataset_id(dataset_id: str) -> Sequence[Document]:
+        documents = db.session.scalars(
+            select(Document).where(
                 Document.dataset_id == dataset_id,
                 Document.enabled == True,
             )
-            .all()
-        )
+        ).all()
 
         return documents
 
     @staticmethod
-    def get_working_documents_by_dataset_id(dataset_id: str) -> list[Document]:
-        documents = (
-            db.session.query(Document)
-            .where(
+    def get_working_documents_by_dataset_id(dataset_id: str) -> Sequence[Document]:
+        documents = db.session.scalars(
+            select(Document).where(
                 Document.dataset_id == dataset_id,
                 Document.enabled == True,
                 Document.indexing_status == "completed",
                 Document.archived == False,
             )
-            .all()
-        )
+        ).all()
 
         return documents
 
     @staticmethod
-    def get_error_documents_by_dataset_id(dataset_id: str) -> list[Document]:
-        documents = (
-            db.session.query(Document)
-            .where(Document.dataset_id == dataset_id, Document.indexing_status.in_(["error", "paused"]))
-            .all()
-        )
+    def get_error_documents_by_dataset_id(dataset_id: str) -> Sequence[Document]:
+        documents = db.session.scalars(
+            select(Document).where(Document.dataset_id == dataset_id, Document.indexing_status.in_(["error", "paused"]))
+        ).all()
         return documents
 
     @staticmethod
-    def get_batch_documents(dataset_id: str, batch: str) -> list[Document]:
+    def get_batch_documents(dataset_id: str, batch: str) -> Sequence[Document]:
         assert isinstance(current_user, Account)
-
-        documents = (
-            db.session.query(Document)
-            .where(
+        documents = db.session.scalars(
+            select(Document).where(
                 Document.batch == batch,
                 Document.dataset_id == dataset_id,
                 Document.tenant_id == current_user.current_tenant_id,
             )
-            .all()
-        )
+        ).all()
 
         return documents
 
@@ -984,7 +972,7 @@ class DocumentService:
         # Check if document_ids is not empty to avoid WHERE false condition
         if not document_ids or len(document_ids) == 0:
             return
-        documents = db.session.query(Document).where(Document.id.in_(document_ids)).all()
+        documents = db.session.scalars(select(Document).where(Document.id.in_(document_ids))).all()
         file_ids = [
             document.data_source_info_dict["upload_file_id"]
             for document in documents
@@ -2424,16 +2412,14 @@ class SegmentService:
         if not segment_ids or len(segment_ids) == 0:
             return
         if action == "enable":
-            segments = (
-                db.session.query(DocumentSegment)
-                .where(
+            segments = db.session.scalars(
+                select(DocumentSegment).where(
                     DocumentSegment.id.in_(segment_ids),
                     DocumentSegment.dataset_id == dataset.id,
                     DocumentSegment.document_id == document.id,
                     DocumentSegment.enabled == False,
                 )
-                .all()
-            )
+            ).all()
             if not segments:
                 return
             real_deal_segment_ids = []
@@ -2451,16 +2437,14 @@ class SegmentService:
 
             enable_segments_to_index_task.delay(real_deal_segment_ids, dataset.id, document.id)
         elif action == "disable":
-            segments = (
-                db.session.query(DocumentSegment)
-                .where(
+            segments = db.session.scalars(
+                select(DocumentSegment).where(
                     DocumentSegment.id.in_(segment_ids),
                     DocumentSegment.dataset_id == dataset.id,
                     DocumentSegment.document_id == document.id,
                     DocumentSegment.enabled == True,
                 )
-                .all()
-            )
+            ).all()
             if not segments:
                 return
             real_deal_segment_ids = []
@@ -2532,16 +2516,13 @@ class SegmentService:
         dataset: Dataset,
     ) -> list[ChildChunk]:
         assert isinstance(current_user, Account)
-
-        child_chunks = (
-            db.session.query(ChildChunk)
-            .where(
+        child_chunks = db.session.scalars(
+            select(ChildChunk).where(
                 ChildChunk.dataset_id == dataset.id,
                 ChildChunk.document_id == document.id,
                 ChildChunk.segment_id == segment.id,
             )
-            .all()
-        )
+        ).all()
         child_chunks_map = {chunk.id: chunk for chunk in child_chunks}
 
         new_child_chunks, update_child_chunks, delete_child_chunks, new_child_chunks_args = [], [], [], []
@@ -2751,13 +2732,11 @@ class DatasetCollectionBindingService:
 class DatasetPermissionService:
     @classmethod
     def get_dataset_partial_member_list(cls, dataset_id):
-        user_list_query = (
-            db.session.query(
+        user_list_query = db.session.scalars(
+            select(
                 DatasetPermission.account_id,
-            )
-            .where(DatasetPermission.dataset_id == dataset_id)
-            .all()
-        )
+            ).where(DatasetPermission.dataset_id == dataset_id)
+        ).all()
 
         user_list = []
         for user in user_list_query:
diff --git a/api/services/model_load_balancing_service.py b/api/services/model_load_balancing_service.py
index d0e2230540..33d7dacba0 100644
--- a/api/services/model_load_balancing_service.py
+++ b/api/services/model_load_balancing_service.py
@@ -3,7 +3,7 @@ import logging
 from json import JSONDecodeError
 from typing import Optional, Union
 
-from sqlalchemy import or_
+from sqlalchemy import or_, select
 
 from constants import HIDDEN_VALUE
 from core.entities.provider_configuration import ProviderConfiguration
@@ -322,16 +322,14 @@ class ModelLoadBalancingService:
         if not isinstance(configs, list):
             raise ValueError("Invalid load balancing configs")
 
-        current_load_balancing_configs = (
-            db.session.query(LoadBalancingModelConfig)
-            .where(
+        current_load_balancing_configs = db.session.scalars(
+            select(LoadBalancingModelConfig).where(
                 LoadBalancingModelConfig.tenant_id == tenant_id,
                 LoadBalancingModelConfig.provider_name == provider_configuration.provider.provider,
                 LoadBalancingModelConfig.model_type == model_type_enum.to_origin_model_type(),
                 LoadBalancingModelConfig.model_name == model,
             )
-            .all()
-        )
+        ).all()
 
         # id as key, config as value
         current_load_balancing_configs_dict = {config.id: config for config in current_load_balancing_configs}
diff --git a/api/services/recommend_app/database/database_retrieval.py b/api/services/recommend_app/database/database_retrieval.py
index e19f53f120..a9733e0826 100644
--- a/api/services/recommend_app/database/database_retrieval.py
+++ b/api/services/recommend_app/database/database_retrieval.py
@@ -1,5 +1,7 @@
 from typing import Optional
 
+from sqlalchemy import select
+
 from constants.languages import languages
 from extensions.ext_database import db
 from models.model import App, RecommendedApp
@@ -31,18 +33,14 @@ class DatabaseRecommendAppRetrieval(RecommendAppRetrievalBase):
         :param language: language
         :return:
         """
-        recommended_apps = (
-            db.session.query(RecommendedApp)
-            .where(RecommendedApp.is_listed == True, RecommendedApp.language == language)
-            .all()
-        )
+        recommended_apps = db.session.scalars(
+            select(RecommendedApp).where(RecommendedApp.is_listed == True, RecommendedApp.language == language)
+        ).all()
 
         if len(recommended_apps) == 0:
-            recommended_apps = (
-                db.session.query(RecommendedApp)
-                .where(RecommendedApp.is_listed == True, RecommendedApp.language == languages[0])
-                .all()
-            )
+            recommended_apps = db.session.scalars(
+                select(RecommendedApp).where(RecommendedApp.is_listed == True, RecommendedApp.language == languages[0])
+            ).all()
 
         categories = set()
         recommended_apps_result = []
diff --git a/api/services/tag_service.py b/api/services/tag_service.py
index a16bdb46cd..dd67b19966 100644
--- a/api/services/tag_service.py
+++ b/api/services/tag_service.py
@@ -2,7 +2,7 @@ import uuid
 from typing import Optional
 
 from flask_login import current_user
-from sqlalchemy import func
+from sqlalchemy import func, select
 from werkzeug.exceptions import NotFound
 
 from extensions.ext_database import db
@@ -29,35 +29,30 @@ class TagService:
         # Check if tag_ids is not empty to avoid WHERE false condition
         if not tag_ids or len(tag_ids) == 0:
             return []
-        tags = (
-            db.session.query(Tag)
-            .where(Tag.id.in_(tag_ids), Tag.tenant_id == current_tenant_id, Tag.type == tag_type)
-            .all()
-        )
+        tags = db.session.scalars(
+            select(Tag).where(Tag.id.in_(tag_ids), Tag.tenant_id == current_tenant_id, Tag.type == tag_type)
+        ).all()
         if not tags:
             return []
         tag_ids = [tag.id for tag in tags]
         # Check if tag_ids is not empty to avoid WHERE false condition
         if not tag_ids or len(tag_ids) == 0:
             return []
-        tag_bindings = (
-            db.session.query(TagBinding.target_id)
-            .where(TagBinding.tag_id.in_(tag_ids), TagBinding.tenant_id == current_tenant_id)
-            .all()
-        )
-        if not tag_bindings:
-            return []
-        results = [tag_binding.target_id for tag_binding in tag_bindings]
-        return results
+        tag_bindings = db.session.scalars(
+            select(TagBinding.target_id).where(
+                TagBinding.tag_id.in_(tag_ids), TagBinding.tenant_id == current_tenant_id
+            )
+        ).all()
+        return tag_bindings
 
     @staticmethod
     def get_tag_by_tag_name(tag_type: str, current_tenant_id: str, tag_name: str):
         if not tag_type or not tag_name:
             return []
-        tags = (
-            db.session.query(Tag)
-            .where(Tag.name == tag_name, Tag.tenant_id == current_tenant_id, Tag.type == tag_type)
-            .all()
+        tags = list(
+            db.session.scalars(
+                select(Tag).where(Tag.name == tag_name, Tag.tenant_id == current_tenant_id, Tag.type == tag_type)
+            ).all()
         )
         if not tags:
             return []
@@ -117,7 +112,7 @@ class TagService:
             raise NotFound("Tag not found")
         db.session.delete(tag)
         # delete tag binding
-        tag_bindings = db.session.query(TagBinding).where(TagBinding.tag_id == tag_id).all()
+        tag_bindings = db.session.scalars(select(TagBinding).where(TagBinding.tag_id == tag_id)).all()
         if tag_bindings:
             for tag_binding in tag_bindings:
                 db.session.delete(tag_binding)
diff --git a/api/services/tools/api_tools_manage_service.py b/api/services/tools/api_tools_manage_service.py
index 78e587abee..f86d7e51bf 100644
--- a/api/services/tools/api_tools_manage_service.py
+++ b/api/services/tools/api_tools_manage_service.py
@@ -4,6 +4,7 @@ from collections.abc import Mapping
 from typing import Any, cast
 
 from httpx import get
+from sqlalchemy import select
 
 from core.entities.provider_entities import ProviderConfig
 from core.model_runtime.utils.encoders import jsonable_encoder
@@ -443,9 +444,7 @@ class ApiToolManageService:
         list api tools
         """
         # get all api providers
-        db_providers: list[ApiToolProvider] = (
-            db.session.query(ApiToolProvider).where(ApiToolProvider.tenant_id == tenant_id).all() or []
-        )
+        db_providers = db.session.scalars(select(ApiToolProvider).where(ApiToolProvider.tenant_id == tenant_id)).all()
 
         result: list[ToolProviderApiEntity] = []
 
diff --git a/api/services/tools/workflow_tools_manage_service.py b/api/services/tools/workflow_tools_manage_service.py
index 2f8a91ed82..2449536d5c 100644
--- a/api/services/tools/workflow_tools_manage_service.py
+++ b/api/services/tools/workflow_tools_manage_service.py
@@ -3,7 +3,7 @@ from collections.abc import Mapping
 from datetime import datetime
 from typing import Any
 
-from sqlalchemy import or_
+from sqlalchemy import or_, select
 
 from core.model_runtime.utils.encoders import jsonable_encoder
 from core.tools.__base.tool_provider import ToolProviderController
@@ -186,7 +186,9 @@ class WorkflowToolManageService:
         :param tenant_id: the tenant id
         :return: the list of tools
         """
-        db_tools = db.session.query(WorkflowToolProvider).where(WorkflowToolProvider.tenant_id == tenant_id).all()
+        db_tools = db.session.scalars(
+            select(WorkflowToolProvider).where(WorkflowToolProvider.tenant_id == tenant_id)
+        ).all()
 
         tools: list[WorkflowToolProviderController] = []
         for provider in db_tools:
diff --git a/api/tasks/annotation/enable_annotation_reply_task.py b/api/tasks/annotation/enable_annotation_reply_task.py
index 3498e08426..cdc07c77a8 100644
--- a/api/tasks/annotation/enable_annotation_reply_task.py
+++ b/api/tasks/annotation/enable_annotation_reply_task.py
@@ -3,6 +3,7 @@ import time
 
 import click
 from celery import shared_task
+from sqlalchemy import select
 
 from core.rag.datasource.vdb.vector_factory import Vector
 from core.rag.models.document import Document
@@ -39,7 +40,7 @@ def enable_annotation_reply_task(
         db.session.close()
         return
 
-    annotations = db.session.query(MessageAnnotation).where(MessageAnnotation.app_id == app_id).all()
+    annotations = db.session.scalars(select(MessageAnnotation).where(MessageAnnotation.app_id == app_id)).all()
     enable_app_annotation_key = f"enable_app_annotation_{str(app_id)}"
     enable_app_annotation_job_key = f"enable_app_annotation_job_{str(job_id)}"
 
diff --git a/api/tasks/batch_clean_document_task.py b/api/tasks/batch_clean_document_task.py
index 08e2c4a556..212f8c3c6a 100644
--- a/api/tasks/batch_clean_document_task.py
+++ b/api/tasks/batch_clean_document_task.py
@@ -3,6 +3,7 @@ import time
 
 import click
 from celery import shared_task
+from sqlalchemy import select
 
 from core.rag.index_processor.index_processor_factory import IndexProcessorFactory
 from core.tools.utils.web_reader_tool import get_image_upload_file_ids
@@ -34,7 +35,9 @@ def batch_clean_document_task(document_ids: list[str], dataset_id: str, doc_form
         if not dataset:
             raise Exception("Document has no dataset")
 
-        segments = db.session.query(DocumentSegment).where(DocumentSegment.document_id.in_(document_ids)).all()
+        segments = db.session.scalars(
+            select(DocumentSegment).where(DocumentSegment.document_id.in_(document_ids))
+        ).all()
         # check segment is exist
         if segments:
             index_node_ids = [segment.index_node_id for segment in segments]
@@ -59,7 +62,7 @@ def batch_clean_document_task(document_ids: list[str], dataset_id: str, doc_form
 
             db.session.commit()
         if file_ids:
-            files = db.session.query(UploadFile).where(UploadFile.id.in_(file_ids)).all()
+            files = db.session.scalars(select(UploadFile).where(UploadFile.id.in_(file_ids))).all()
             for file in files:
                 try:
                     storage.delete(file.key)
diff --git a/api/tasks/clean_dataset_task.py b/api/tasks/clean_dataset_task.py
index 9d12b6a589..5f2a355d16 100644
--- a/api/tasks/clean_dataset_task.py
+++ b/api/tasks/clean_dataset_task.py
@@ -3,6 +3,7 @@ import time
 
 import click
 from celery import shared_task
+from sqlalchemy import select
 
 from core.rag.index_processor.index_processor_factory import IndexProcessorFactory
 from core.tools.utils.web_reader_tool import get_image_upload_file_ids
@@ -55,8 +56,8 @@ def clean_dataset_task(
             index_struct=index_struct,
             collection_binding_id=collection_binding_id,
         )
-        documents = db.session.query(Document).where(Document.dataset_id == dataset_id).all()
-        segments = db.session.query(DocumentSegment).where(DocumentSegment.dataset_id == dataset_id).all()
+        documents = db.session.scalars(select(Document).where(Document.dataset_id == dataset_id)).all()
+        segments = db.session.scalars(select(DocumentSegment).where(DocumentSegment.dataset_id == dataset_id)).all()
 
         # Enhanced validation: Check if doc_form is None, empty string, or contains only whitespace
         # This ensures all invalid doc_form values are properly handled
diff --git a/api/tasks/clean_document_task.py b/api/tasks/clean_document_task.py
index 6549ad04b5..761ac6fc3d 100644
--- a/api/tasks/clean_document_task.py
+++ b/api/tasks/clean_document_task.py
@@ -4,6 +4,7 @@ from typing import Optional
 
 import click
 from celery import shared_task
+from sqlalchemy import select
 
 from core.rag.index_processor.index_processor_factory import IndexProcessorFactory
 from core.tools.utils.web_reader_tool import get_image_upload_file_ids
@@ -35,7 +36,7 @@ def clean_document_task(document_id: str, dataset_id: str, doc_form: str, file_i
         if not dataset:
             raise Exception("Document has no dataset")
 
-        segments = db.session.query(DocumentSegment).where(DocumentSegment.document_id == document_id).all()
+        segments = db.session.scalars(select(DocumentSegment).where(DocumentSegment.document_id == document_id)).all()
         # check segment is exist
         if segments:
             index_node_ids = [segment.index_node_id for segment in segments]
diff --git a/api/tasks/clean_notion_document_task.py b/api/tasks/clean_notion_document_task.py
index e7a61e22f2..771b43f9b0 100644
--- a/api/tasks/clean_notion_document_task.py
+++ b/api/tasks/clean_notion_document_task.py
@@ -3,6 +3,7 @@ import time
 
 import click
 from celery import shared_task
+from sqlalchemy import select
 
 from core.rag.index_processor.index_processor_factory import IndexProcessorFactory
 from extensions.ext_database import db
@@ -34,7 +35,9 @@ def clean_notion_document_task(document_ids: list[str], dataset_id: str):
             document = db.session.query(Document).where(Document.id == document_id).first()
             db.session.delete(document)
 
-            segments = db.session.query(DocumentSegment).where(DocumentSegment.document_id == document_id).all()
+            segments = db.session.scalars(
+                select(DocumentSegment).where(DocumentSegment.document_id == document_id)
+            ).all()
             index_node_ids = [segment.index_node_id for segment in segments]
 
             index_processor.clean(dataset, index_node_ids, with_keywords=True, delete_child_chunks=True)
diff --git a/api/tasks/deal_dataset_vector_index_task.py b/api/tasks/deal_dataset_vector_index_task.py
index 23e929c57e..dc6ef6fb61 100644
--- a/api/tasks/deal_dataset_vector_index_task.py
+++ b/api/tasks/deal_dataset_vector_index_task.py
@@ -4,6 +4,7 @@ from typing import Literal
 
 import click
 from celery import shared_task
+from sqlalchemy import select
 
 from core.rag.index_processor.constant.index_type import IndexType
 from core.rag.index_processor.index_processor_factory import IndexProcessorFactory
@@ -36,16 +37,14 @@ def deal_dataset_vector_index_task(dataset_id: str, action: Literal["remove", "a
         if action == "remove":
             index_processor.clean(dataset, None, with_keywords=False)
         elif action == "add":
-            dataset_documents = (
-                db.session.query(DatasetDocument)
-                .where(
+            dataset_documents = db.session.scalars(
+                select(DatasetDocument).where(
                     DatasetDocument.dataset_id == dataset_id,
                     DatasetDocument.indexing_status == "completed",
                     DatasetDocument.enabled == True,
                     DatasetDocument.archived == False,
                 )
-                .all()
-            )
+            ).all()
 
             if dataset_documents:
                 dataset_documents_ids = [doc.id for doc in dataset_documents]
@@ -89,16 +88,14 @@ def deal_dataset_vector_index_task(dataset_id: str, action: Literal["remove", "a
                         )
                         db.session.commit()
         elif action == "update":
-            dataset_documents = (
-                db.session.query(DatasetDocument)
-                .where(
+            dataset_documents = db.session.scalars(
+                select(DatasetDocument).where(
                     DatasetDocument.dataset_id == dataset_id,
                     DatasetDocument.indexing_status == "completed",
                     DatasetDocument.enabled == True,
                     DatasetDocument.archived == False,
                 )
-                .all()
-            )
+            ).all()
             # add new index
             if dataset_documents:
                 # update document status
diff --git a/api/tasks/disable_segments_from_index_task.py b/api/tasks/disable_segments_from_index_task.py
index d4899fe0e4..9038dc179b 100644
--- a/api/tasks/disable_segments_from_index_task.py
+++ b/api/tasks/disable_segments_from_index_task.py
@@ -3,6 +3,7 @@ import time
 
 import click
 from celery import shared_task
+from sqlalchemy import select
 
 from core.rag.index_processor.index_processor_factory import IndexProcessorFactory
 from extensions.ext_database import db
@@ -44,15 +45,13 @@ def disable_segments_from_index_task(segment_ids: list, dataset_id: str, documen
     # sync index processor
     index_processor = IndexProcessorFactory(dataset_document.doc_form).init_index_processor()
 
-    segments = (
-        db.session.query(DocumentSegment)
-        .where(
+    segments = db.session.scalars(
+        select(DocumentSegment).where(
             DocumentSegment.id.in_(segment_ids),
             DocumentSegment.dataset_id == dataset_id,
             DocumentSegment.document_id == document_id,
         )
-        .all()
-    )
+    ).all()
 
     if not segments:
         db.session.close()
diff --git a/api/tasks/document_indexing_sync_task.py b/api/tasks/document_indexing_sync_task.py
index 687e3e9551..24d7d16578 100644
--- a/api/tasks/document_indexing_sync_task.py
+++ b/api/tasks/document_indexing_sync_task.py
@@ -3,6 +3,7 @@ import time
 
 import click
 from celery import shared_task
+from sqlalchemy import select
 
 from core.indexing_runner import DocumentIsPausedError, IndexingRunner
 from core.rag.extractor.notion_extractor import NotionExtractor
@@ -85,7 +86,9 @@ def document_indexing_sync_task(dataset_id: str, document_id: str):
                 index_type = document.doc_form
                 index_processor = IndexProcessorFactory(index_type).init_index_processor()
 
-                segments = db.session.query(DocumentSegment).where(DocumentSegment.document_id == document_id).all()
+                segments = db.session.scalars(
+                    select(DocumentSegment).where(DocumentSegment.document_id == document_id)
+                ).all()
                 index_node_ids = [segment.index_node_id for segment in segments]
 
                 # delete from vector index
diff --git a/api/tasks/document_indexing_update_task.py b/api/tasks/document_indexing_update_task.py
index 48566b6104..161502a228 100644
--- a/api/tasks/document_indexing_update_task.py
+++ b/api/tasks/document_indexing_update_task.py
@@ -3,6 +3,7 @@ import time
 
 import click
 from celery import shared_task
+from sqlalchemy import select
 
 from core.indexing_runner import DocumentIsPausedError, IndexingRunner
 from core.rag.index_processor.index_processor_factory import IndexProcessorFactory
@@ -45,7 +46,7 @@ def document_indexing_update_task(dataset_id: str, document_id: str):
         index_type = document.doc_form
         index_processor = IndexProcessorFactory(index_type).init_index_processor()
 
-        segments = db.session.query(DocumentSegment).where(DocumentSegment.document_id == document_id).all()
+        segments = db.session.scalars(select(DocumentSegment).where(DocumentSegment.document_id == document_id)).all()
         if segments:
             index_node_ids = [segment.index_node_id for segment in segments]
 
diff --git a/api/tasks/duplicate_document_indexing_task.py b/api/tasks/duplicate_document_indexing_task.py
index d93f30ba37..2020179cd9 100644
--- a/api/tasks/duplicate_document_indexing_task.py
+++ b/api/tasks/duplicate_document_indexing_task.py
@@ -3,6 +3,7 @@ import time
 
 import click
 from celery import shared_task
+from sqlalchemy import select
 
 from configs import dify_config
 from core.indexing_runner import DocumentIsPausedError, IndexingRunner
@@ -79,7 +80,9 @@ def duplicate_document_indexing_task(dataset_id: str, document_ids: list):
                 index_type = document.doc_form
                 index_processor = IndexProcessorFactory(index_type).init_index_processor()
 
-                segments = db.session.query(DocumentSegment).where(DocumentSegment.document_id == document_id).all()
+                segments = db.session.scalars(
+                    select(DocumentSegment).where(DocumentSegment.document_id == document_id)
+                ).all()
                 if segments:
                     index_node_ids = [segment.index_node_id for segment in segments]
 
diff --git a/api/tasks/enable_segments_to_index_task.py b/api/tasks/enable_segments_to_index_task.py
index 647664641d..c5ca7a6171 100644
--- a/api/tasks/enable_segments_to_index_task.py
+++ b/api/tasks/enable_segments_to_index_task.py
@@ -3,6 +3,7 @@ import time
 
 import click
 from celery import shared_task
+from sqlalchemy import select
 
 from core.rag.index_processor.constant.index_type import IndexType
 from core.rag.index_processor.index_processor_factory import IndexProcessorFactory
@@ -45,15 +46,13 @@ def enable_segments_to_index_task(segment_ids: list, dataset_id: str, document_i
     # sync index processor
     index_processor = IndexProcessorFactory(dataset_document.doc_form).init_index_processor()
 
-    segments = (
-        db.session.query(DocumentSegment)
-        .where(
+    segments = db.session.scalars(
+        select(DocumentSegment).where(
             DocumentSegment.id.in_(segment_ids),
             DocumentSegment.dataset_id == dataset_id,
             DocumentSegment.document_id == document_id,
         )
-        .all()
-    )
+    ).all()
     if not segments:
         logger.info(click.style(f"Segments not found: {segment_ids}", fg="cyan"))
         db.session.close()
diff --git a/api/tasks/remove_document_from_index_task.py b/api/tasks/remove_document_from_index_task.py
index ec56ab583b..c0ab2d0b41 100644
--- a/api/tasks/remove_document_from_index_task.py
+++ b/api/tasks/remove_document_from_index_task.py
@@ -3,6 +3,7 @@ import time
 
 import click
 from celery import shared_task
+from sqlalchemy import select
 
 from core.rag.index_processor.index_processor_factory import IndexProcessorFactory
 from extensions.ext_database import db
@@ -45,7 +46,7 @@ def remove_document_from_index_task(document_id: str):
 
         index_processor = IndexProcessorFactory(document.doc_form).init_index_processor()
 
-        segments = db.session.query(DocumentSegment).where(DocumentSegment.document_id == document.id).all()
+        segments = db.session.scalars(select(DocumentSegment).where(DocumentSegment.document_id == document.id)).all()
         index_node_ids = [segment.index_node_id for segment in segments]
         if index_node_ids:
             try:
diff --git a/api/tasks/retry_document_indexing_task.py b/api/tasks/retry_document_indexing_task.py
index c52218caae..b65eca7e0b 100644
--- a/api/tasks/retry_document_indexing_task.py
+++ b/api/tasks/retry_document_indexing_task.py
@@ -3,6 +3,7 @@ import time
 
 import click
 from celery import shared_task
+from sqlalchemy import select
 
 from core.indexing_runner import IndexingRunner
 from core.rag.index_processor.index_processor_factory import IndexProcessorFactory
@@ -69,7 +70,9 @@ def retry_document_indexing_task(dataset_id: str, document_ids: list[str]):
                 # clean old data
                 index_processor = IndexProcessorFactory(document.doc_form).init_index_processor()
 
-                segments = db.session.query(DocumentSegment).where(DocumentSegment.document_id == document_id).all()
+                segments = db.session.scalars(
+                    select(DocumentSegment).where(DocumentSegment.document_id == document_id)
+                ).all()
                 if segments:
                     index_node_ids = [segment.index_node_id for segment in segments]
                     # delete from vector index
diff --git a/api/tasks/sync_website_document_indexing_task.py b/api/tasks/sync_website_document_indexing_task.py
index 3c7c69e3c8..0dc1d841f4 100644
--- a/api/tasks/sync_website_document_indexing_task.py
+++ b/api/tasks/sync_website_document_indexing_task.py
@@ -3,6 +3,7 @@ import time
 
 import click
 from celery import shared_task
+from sqlalchemy import select
 
 from core.indexing_runner import IndexingRunner
 from core.rag.index_processor.index_processor_factory import IndexProcessorFactory
@@ -63,7 +64,7 @@ def sync_website_document_indexing_task(dataset_id: str, document_id: str):
         # clean old data
         index_processor = IndexProcessorFactory(document.doc_form).init_index_processor()
 
-        segments = db.session.query(DocumentSegment).where(DocumentSegment.document_id == document_id).all()
+        segments = db.session.scalars(select(DocumentSegment).where(DocumentSegment.document_id == document_id)).all()
         if segments:
             index_node_ids = [segment.index_node_id for segment in segments]
             # delete from vector index
diff --git a/api/tests/test_containers_integration_tests/services/test_model_load_balancing_service.py b/api/tests/test_containers_integration_tests/services/test_model_load_balancing_service.py
index cb20238f0c..66527dd506 100644
--- a/api/tests/test_containers_integration_tests/services/test_model_load_balancing_service.py
+++ b/api/tests/test_containers_integration_tests/services/test_model_load_balancing_service.py
@@ -2,6 +2,7 @@ from unittest.mock import MagicMock, patch
 
 import pytest
 from faker import Faker
+from sqlalchemy import select
 
 from models.account import TenantAccountJoin, TenantAccountRole
 from models.model import Account, Tenant
@@ -468,7 +469,7 @@ class TestModelLoadBalancingService:
         assert load_balancing_config.id is not None
 
         # Verify inherit config was created in database
-        inherit_configs = (
-            db.session.query(LoadBalancingModelConfig).where(LoadBalancingModelConfig.name == "__inherit__").all()
-        )
+        inherit_configs = db.session.scalars(
+            select(LoadBalancingModelConfig).where(LoadBalancingModelConfig.name == "__inherit__")
+        ).all()
         assert len(inherit_configs) == 1
diff --git a/api/tests/test_containers_integration_tests/services/test_tag_service.py b/api/tests/test_containers_integration_tests/services/test_tag_service.py
index d09a4a17ab..04cff397b2 100644
--- a/api/tests/test_containers_integration_tests/services/test_tag_service.py
+++ b/api/tests/test_containers_integration_tests/services/test_tag_service.py
@@ -2,6 +2,7 @@ from unittest.mock import create_autospec, patch
 
 import pytest
 from faker import Faker
+from sqlalchemy import select
 from werkzeug.exceptions import NotFound
 
 from models.account import Account, Tenant, TenantAccountJoin, TenantAccountRole
@@ -954,7 +955,9 @@ class TestTagService:
         from extensions.ext_database import db
 
         # Verify only one binding exists
-        bindings = db.session.query(TagBinding).where(TagBinding.tag_id == tag.id, TagBinding.target_id == app.id).all()
+        bindings = db.session.scalars(
+            select(TagBinding).where(TagBinding.tag_id == tag.id, TagBinding.target_id == app.id)
+        ).all()
         assert len(bindings) == 1
 
     def test_save_tag_binding_invalid_target_type(self, db_session_with_containers, mock_external_service_dependencies):
@@ -1064,7 +1067,9 @@ class TestTagService:
         # No error should be raised, and database state should remain unchanged
         from extensions.ext_database import db
 
-        bindings = db.session.query(TagBinding).where(TagBinding.tag_id == tag.id, TagBinding.target_id == app.id).all()
+        bindings = db.session.scalars(
+            select(TagBinding).where(TagBinding.tag_id == tag.id, TagBinding.target_id == app.id)
+        ).all()
         assert len(bindings) == 0
 
     def test_check_target_exists_knowledge_success(
diff --git a/api/tests/test_containers_integration_tests/services/test_web_conversation_service.py b/api/tests/test_containers_integration_tests/services/test_web_conversation_service.py
index 6d6f1dab72..c9ace46c55 100644
--- a/api/tests/test_containers_integration_tests/services/test_web_conversation_service.py
+++ b/api/tests/test_containers_integration_tests/services/test_web_conversation_service.py
@@ -2,6 +2,7 @@ from unittest.mock import patch
 
 import pytest
 from faker import Faker
+from sqlalchemy import select
 
 from core.app.entities.app_invoke_entities import InvokeFrom
 from models.account import Account
@@ -354,16 +355,14 @@ class TestWebConversationService:
         # Verify only one pinned conversation record exists
         from extensions.ext_database import db
 
-        pinned_conversations = (
-            db.session.query(PinnedConversation)
-            .where(
+        pinned_conversations = db.session.scalars(
+            select(PinnedConversation).where(
                 PinnedConversation.app_id == app.id,
                 PinnedConversation.conversation_id == conversation.id,
                 PinnedConversation.created_by_role == "account",
                 PinnedConversation.created_by == account.id,
             )
-            .all()
-        )
+        ).all()
 
         assert len(pinned_conversations) == 1
 
diff --git a/api/tests/unit_tests/services/auth/test_api_key_auth_service.py b/api/tests/unit_tests/services/auth/test_api_key_auth_service.py
index dc42a04cf3..d23298f096 100644
--- a/api/tests/unit_tests/services/auth/test_api_key_auth_service.py
+++ b/api/tests/unit_tests/services/auth/test_api_key_auth_service.py
@@ -28,18 +28,20 @@ class TestApiKeyAuthService:
         mock_binding.provider = self.provider
         mock_binding.disabled = False
 
-        mock_session.query.return_value.where.return_value.all.return_value = [mock_binding]
+        mock_session.scalars.return_value.all.return_value = [mock_binding]
 
         result = ApiKeyAuthService.get_provider_auth_list(self.tenant_id)
 
         assert len(result) == 1
         assert result[0].tenant_id == self.tenant_id
-        mock_session.query.assert_called_once_with(DataSourceApiKeyAuthBinding)
+        assert mock_session.scalars.call_count == 1
+        select_arg = mock_session.scalars.call_args[0][0]
+        assert "data_source_api_key_auth_binding" in str(select_arg).lower()
 
     @patch("services.auth.api_key_auth_service.db.session")
     def test_get_provider_auth_list_empty(self, mock_session):
         """Test get provider auth list - empty result"""
-        mock_session.query.return_value.where.return_value.all.return_value = []
+        mock_session.scalars.return_value.all.return_value = []
 
         result = ApiKeyAuthService.get_provider_auth_list(self.tenant_id)
 
@@ -48,13 +50,15 @@ class TestApiKeyAuthService:
     @patch("services.auth.api_key_auth_service.db.session")
     def test_get_provider_auth_list_filters_disabled(self, mock_session):
         """Test get provider auth list - filters disabled items"""
-        mock_session.query.return_value.where.return_value.all.return_value = []
+        mock_session.scalars.return_value.all.return_value = []
 
         ApiKeyAuthService.get_provider_auth_list(self.tenant_id)
-
-        # Verify where conditions include disabled.is_(False)
-        where_call = mock_session.query.return_value.where.call_args[0]
-        assert len(where_call) == 2  # tenant_id and disabled filter conditions
+        select_stmt = mock_session.scalars.call_args[0][0]
+        where_clauses = list(getattr(select_stmt, "_where_criteria", []) or [])
+        # Ensure both tenant filter and disabled filter exist
+        where_strs = [str(c).lower() for c in where_clauses]
+        assert any("tenant_id" in s for s in where_strs)
+        assert any("disabled" in s for s in where_strs)
 
     @patch("services.auth.api_key_auth_service.db.session")
     @patch("services.auth.api_key_auth_service.ApiKeyAuthFactory")
diff --git a/api/tests/unit_tests/services/auth/test_auth_integration.py b/api/tests/unit_tests/services/auth/test_auth_integration.py
index 4ce5525942..bb39b92c09 100644
--- a/api/tests/unit_tests/services/auth/test_auth_integration.py
+++ b/api/tests/unit_tests/services/auth/test_auth_integration.py
@@ -63,10 +63,10 @@ class TestAuthIntegration:
         tenant1_binding = self._create_mock_binding(self.tenant_id_1, AuthType.FIRECRAWL, self.firecrawl_credentials)
         tenant2_binding = self._create_mock_binding(self.tenant_id_2, AuthType.JINA, self.jina_credentials)
 
-        mock_session.query.return_value.where.return_value.all.return_value = [tenant1_binding]
+        mock_session.scalars.return_value.all.return_value = [tenant1_binding]
         result1 = ApiKeyAuthService.get_provider_auth_list(self.tenant_id_1)
 
-        mock_session.query.return_value.where.return_value.all.return_value = [tenant2_binding]
+        mock_session.scalars.return_value.all.return_value = [tenant2_binding]
         result2 = ApiKeyAuthService.get_provider_auth_list(self.tenant_id_2)
 
         assert len(result1) == 1