diff --git a/api/.importlinter b/api/.importlinter
index 57773f57d6..5c0a6e1288 100644
--- a/api/.importlinter
+++ b/api/.importlinter
@@ -45,7 +45,6 @@ allow_indirect_imports = True
 ignore_imports =
     dify_graph.nodes.agent.agent_node -> extensions.ext_database
     dify_graph.nodes.llm.node -> extensions.ext_database
-    dify_graph.nodes.tool.tool_node -> extensions.ext_database
     dify_graph.model_runtime.model_providers.__base.ai_model -> extensions.ext_redis
     dify_graph.model_runtime.model_providers.model_provider_factory -> extensions.ext_redis
 
@@ -111,7 +110,6 @@ ignore_imports =
     dify_graph.nodes.parameter_extractor.parameter_extractor_node -> core.model_manager
     dify_graph.nodes.question_classifier.question_classifier_node -> core.model_manager
     dify_graph.nodes.tool.tool_node -> core.tools.utils.message_transformer
-    dify_graph.nodes.tool.tool_node -> models
     dify_graph.nodes.agent.agent_node -> models.model
     dify_graph.nodes.llm.node -> core.helper.code_executor
     dify_graph.nodes.llm.node -> core.llm_generator.output_parser.errors
@@ -134,7 +132,6 @@ ignore_imports =
     dify_graph.nodes.tool.tool_node -> core.tools.errors
     dify_graph.nodes.agent.agent_node -> extensions.ext_database
     dify_graph.nodes.llm.node -> extensions.ext_database
-    dify_graph.nodes.tool.tool_node -> extensions.ext_database
     dify_graph.nodes.agent.agent_node -> models
     dify_graph.nodes.llm.node -> models.model
     dify_graph.nodes.agent.agent_node -> services
diff --git a/api/core/tools/tool_file_manager.py b/api/core/tools/tool_file_manager.py
index d16b919561..f6eccc734b 100644
--- a/api/core/tools/tool_file_manager.py
+++ b/api/core/tools/tool_file_manager.py
@@ -14,6 +14,7 @@ import httpx
 from configs import dify_config
 from core.db.session_factory import session_factory
 from core.helper import ssrf_proxy
+from dify_graph.file.models import ToolFile as ToolFilePydanticModel
 from extensions.ext_storage import storage
 from models.model import MessageFile
 from models.tools import ToolFile
@@ -207,7 +208,9 @@ class ToolFileManager:
 
         return blob, tool_file.mimetype
 
-    def get_file_generator_by_tool_file_id(self, tool_file_id: str) -> tuple[Generator | None, ToolFile | None]:
+    def get_file_generator_by_tool_file_id(
+        self, tool_file_id: str
+    ) -> tuple[Generator | None, ToolFilePydanticModel | None]:
         """
         get file binary
 
@@ -229,7 +232,7 @@ class ToolFileManager:
 
         stream = storage.load_stream(tool_file.file_key)
 
-        return stream, tool_file
+        return stream, ToolFilePydanticModel.model_validate(tool_file)
 
 
 # init tool_file_parser
diff --git a/api/core/workflow/node_factory.py b/api/core/workflow/node_factory.py
index c1475f2f18..8c6b1dedee 100644
--- a/api/core/workflow/node_factory.py
+++ b/api/core/workflow/node_factory.py
@@ -50,6 +50,7 @@ from dify_graph.nodes.template_transform.template_renderer import (
     CodeExecutorJinja2TemplateRenderer,
 )
 from dify_graph.nodes.template_transform.template_transform_node import TemplateTransformNode
+from dify_graph.nodes.tool.tool_node import ToolNode
 from dify_graph.variables.segments import StringSegment
 from extensions.ext_database import db
 from models.model import Conversation
@@ -310,6 +311,15 @@ class DifyNodeFactory(NodeFactory):
                 memory=memory,
             )
 
+        if node_type == NodeType.TOOL:
+            return ToolNode(
+                id=node_id,
+                config=node_config,
+                graph_init_params=self.graph_init_params,
+                graph_runtime_state=self.graph_runtime_state,
+                tool_file_manager_factory=self._http_request_tool_file_manager_factory(),
+            )
+
         return node_class(
             id=node_id,
             config=node_config,
diff --git a/api/dify_graph/file/models.py b/api/dify_graph/file/models.py
index db12d4f57a..dcba00978e 100644
--- a/api/dify_graph/file/models.py
+++ b/api/dify_graph/file/models.py
@@ -2,6 +2,7 @@ from __future__ import annotations
 
 from collections.abc import Mapping, Sequence
 from typing import Any
+from uuid import UUID, uuid4
 
 from pydantic import BaseModel, Field, model_validator
 
@@ -43,6 +44,24 @@ class FileUploadConfig(BaseModel):
     number_limits: int = 0
 
 
+class ToolFile(BaseModel):
+    id: UUID = Field(default_factory=uuid4, description="Unique identifier for the file")
+    user_id: UUID = Field(..., description="ID of the user who owns this file")
+    tenant_id: UUID = Field(..., description="ID of the tenant/organization")
+    conversation_id: UUID | None = Field(None, description="ID of the associated conversation")
+    file_key: str = Field(..., max_length=255, description="Storage key for the file")
+    mimetype: str = Field(..., max_length=255, description="MIME type of the file")
+    original_url: str | None = Field(
+        None, max_length=2048, description="Original URL if file was fetched from external source"
+    )
+    name: str = Field(default="", max_length=255, description="Display name of the file")
+    size: int = Field(default=-1, ge=-1, description="File size in bytes (-1 if unknown)")
+
+    class Config:
+        from_attributes = True  # Enable ORM mode for SQLAlchemy compatibility
+        populate_by_name = True
+
+
 class File(BaseModel):
     # NOTE: dify_model_identity is a special identifier used to distinguish between
     # new and old data formats during serialization and deserialization.
diff --git a/api/dify_graph/nodes/protocols.py b/api/dify_graph/nodes/protocols.py
index cc007150f1..62d3bcdca1 100644
--- a/api/dify_graph/nodes/protocols.py
+++ b/api/dify_graph/nodes/protocols.py
@@ -1,8 +1,10 @@
+from collections.abc import Generator
 from typing import Any, Protocol
 
 import httpx
 
 from dify_graph.file import File
+from dify_graph.file.models import ToolFile
 
 
 class HttpClientProtocol(Protocol):
@@ -40,3 +42,5 @@ class ToolFileManagerProtocol(Protocol):
         mimetype: str,
         filename: str | None = None,
     ) -> Any: ...
+
+    def get_file_generator_by_tool_file_id(self, tool_file_id: str) -> tuple[Generator | None, ToolFile | None]: ...
diff --git a/api/dify_graph/nodes/tool/tool_node.py b/api/dify_graph/nodes/tool/tool_node.py
index 57fb946559..a6e0b710f1 100644
--- a/api/dify_graph/nodes/tool/tool_node.py
+++ b/api/dify_graph/nodes/tool/tool_node.py
@@ -1,9 +1,6 @@
 from collections.abc import Generator, Mapping, Sequence
 from typing import TYPE_CHECKING, Any
 
-from sqlalchemy import select
-from sqlalchemy.orm import Session
-
 from core.callback_handler.workflow_tool_callback_handler import DifyWorkflowCallbackHandler
 from core.tools.__base.tool import Tool
 from core.tools.entities.tool_entities import ToolInvokeMessage, ToolParameter
@@ -21,11 +18,10 @@ from dify_graph.model_runtime.entities.llm_entities import LLMUsage
 from dify_graph.node_events import NodeEventBase, NodeRunResult, StreamChunkEvent, StreamCompletedEvent
 from dify_graph.nodes.base.node import Node
 from dify_graph.nodes.base.variable_template_parser import VariableTemplateParser
+from dify_graph.nodes.protocols import ToolFileManagerProtocol
 from dify_graph.variables.segments import ArrayAnySegment, ArrayFileSegment
 from dify_graph.variables.variables import ArrayAnyVariable
-from extensions.ext_database import db
 from factories import file_factory
-from models import ToolFile
 from services.tools.builtin_tools_manage_service import BuiltinToolManageService
 
 from .entities import ToolNodeData
@@ -36,7 +32,8 @@ from .exc import (
 )
 
 if TYPE_CHECKING:
-    from dify_graph.runtime import VariablePool
+    from dify_graph.entities import GraphInitParams
+    from dify_graph.runtime import GraphRuntimeState, VariablePool
 
 
 class ToolNode(Node[ToolNodeData]):
@@ -46,6 +43,23 @@ class ToolNode(Node[ToolNodeData]):
 
     node_type = NodeType.TOOL
 
+    def __init__(
+        self,
+        id: str,
+        config: Mapping[str, Any],
+        graph_init_params: "GraphInitParams",
+        graph_runtime_state: "GraphRuntimeState",
+        *,
+        tool_file_manager_factory: ToolFileManagerProtocol,
+    ):
+        super().__init__(
+            id=id,
+            config=config,
+            graph_init_params=graph_init_params,
+            graph_runtime_state=graph_runtime_state,
+        )
+        self._tool_file_manager_factory = tool_file_manager_factory
+
     @classmethod
     def version(cls) -> str:
         return "1"
@@ -271,11 +285,9 @@ class ToolNode(Node[ToolNodeData]):
 
                 tool_file_id = str(url).split("/")[-1].split(".")[0]
 
-                with Session(db.engine) as session:
-                    stmt = select(ToolFile).where(ToolFile.id == tool_file_id)
-                    tool_file = session.scalar(stmt)
-                    if tool_file is None:
-                        raise ToolFileError(f"Tool file {tool_file_id} does not exist")
+                _, tool_file = self._tool_file_manager_factory.get_file_generator_by_tool_file_id(tool_file_id)
+                if not tool_file:
+                    raise ToolFileError(f"tool file {tool_file_id} not found")
 
                 mapping = {
                     "tool_file_id": tool_file_id,
@@ -294,11 +306,9 @@ class ToolNode(Node[ToolNodeData]):
                 assert message.meta
 
                 tool_file_id = message.message.text.split("/")[-1].split(".")[0]
-                with Session(db.engine) as session:
-                    stmt = select(ToolFile).where(ToolFile.id == tool_file_id)
-                    tool_file = session.scalar(stmt)
-                    if tool_file is None:
-                        raise ToolFileError(f"tool file {tool_file_id} not exists")
+                _, tool_file = self._tool_file_manager_factory.get_file_generator_by_tool_file_id(tool_file_id)
+                if not tool_file:
+                    raise ToolFileError(f"tool file {tool_file_id} not exists")
 
                 mapping = {
                     "tool_file_id": tool_file_id,
diff --git a/api/tests/integration_tests/workflow/nodes/test_tool.py b/api/tests/integration_tests/workflow/nodes/test_tool.py
index f70bf46979..23cb56d2a5 100644
--- a/api/tests/integration_tests/workflow/nodes/test_tool.py
+++ b/api/tests/integration_tests/workflow/nodes/test_tool.py
@@ -8,6 +8,7 @@ from core.workflow.node_factory import DifyNodeFactory
 from dify_graph.enums import WorkflowNodeExecutionStatus
 from dify_graph.graph import Graph
 from dify_graph.node_events import StreamCompletedEvent
+from dify_graph.nodes.protocols import ToolFileManagerProtocol
 from dify_graph.nodes.tool.tool_node import ToolNode
 from dify_graph.runtime import GraphRuntimeState, VariablePool
 from dify_graph.system_variable import SystemVariable
@@ -55,11 +56,14 @@ def init_tool_node(config: dict):
 
     graph = Graph.init(graph_config=graph_config, node_factory=node_factory)
 
+    tool_file_manager_factory = MagicMock(spec=ToolFileManagerProtocol)
+
     node = ToolNode(
         id=str(uuid.uuid4()),
         config=config,
         graph_init_params=init_params,
         graph_runtime_state=graph_runtime_state,
+        tool_file_manager_factory=tool_file_manager_factory,
     )
     return node
 
diff --git a/api/tests/unit_tests/core/workflow/graph_engine/test_mock_nodes.py b/api/tests/unit_tests/core/workflow/graph_engine/test_mock_nodes.py
index 43fadadbc2..34e714a227 100644
--- a/api/tests/unit_tests/core/workflow/graph_engine/test_mock_nodes.py
+++ b/api/tests/unit_tests/core/workflow/graph_engine/test_mock_nodes.py
@@ -22,7 +22,7 @@ from dify_graph.nodes.knowledge_retrieval import KnowledgeRetrievalNode
 from dify_graph.nodes.llm import LLMNode
 from dify_graph.nodes.llm.protocols import CredentialsProvider, ModelFactory
 from dify_graph.nodes.parameter_extractor import ParameterExtractorNode
-from dify_graph.nodes.protocols import HttpClientProtocol
+from dify_graph.nodes.protocols import HttpClientProtocol, ToolFileManagerProtocol
 from dify_graph.nodes.question_classifier import QuestionClassifierNode
 from dify_graph.nodes.template_transform import TemplateTransformNode
 from dify_graph.nodes.template_transform.template_renderer import (
@@ -73,6 +73,12 @@ class MockNodeMixin:
         if isinstance(self, TemplateTransformNode):
             kwargs.setdefault("template_renderer", _TestJinja2Renderer())
 
+        # Provide default tool_file_manager_factory for ToolNode subclasses
+        from dify_graph.nodes.tool import ToolNode as _ToolNode  # local import to avoid cycles
+
+        if isinstance(self, _ToolNode):
+            kwargs.setdefault("tool_file_manager_factory", MagicMock(spec=ToolFileManagerProtocol))
+
         super().__init__(
             id=id,
             config=config,
diff --git a/api/tests/unit_tests/core/workflow/nodes/tool/test_tool_node.py b/api/tests/unit_tests/core/workflow/nodes/tool/test_tool_node.py
index 11554169e1..3cbd96dfef 100644
--- a/api/tests/unit_tests/core/workflow/nodes/tool/test_tool_node.py
+++ b/api/tests/unit_tests/core/workflow/nodes/tool/test_tool_node.py
@@ -31,6 +31,7 @@ def tool_node(monkeypatch) -> ToolNode:
         ops_stub.TraceTask = object  # pragma: no cover - stub attribute
         monkeypatch.setitem(sys.modules, module_name, ops_stub)
 
+    from dify_graph.nodes.protocols import ToolFileManagerProtocol
     from dify_graph.nodes.tool.tool_node import ToolNode
 
     graph_config: dict[str, Any] = {
@@ -69,11 +70,16 @@ def tool_node(monkeypatch) -> ToolNode:
     graph_runtime_state = GraphRuntimeState(variable_pool=variable_pool, start_at=0.0)
 
     config = graph_config["nodes"][0]
+
+    # Provide a stub ToolFileManager to satisfy the updated ToolNode constructor
+    tool_file_manager_factory = MagicMock(spec=ToolFileManagerProtocol)
+
     node = ToolNode(
         id="node-instance",
         config=config,
         graph_init_params=init_params,
         graph_runtime_state=graph_runtime_state,
+        tool_file_manager_factory=tool_file_manager_factory,
     )
     return node