diff --git a/api/services/annotation_service.py b/api/services/annotation_service.py
index 3239af998e..80dd63bf89 100644
--- a/api/services/annotation_service.py
+++ b/api/services/annotation_service.py
@@ -452,6 +452,11 @@ class AppAnnotationService:
         if not app:
             raise NotFound("App not found")
 
+        # if annotation reply is enabled, delete annotation index
+        app_annotation_setting = (
+            db.session.query(AppAnnotationSetting).where(AppAnnotationSetting.app_id == app_id).first()
+        )
+
         annotations_query = db.session.query(MessageAnnotation).filter(MessageAnnotation.app_id == app_id)
         for annotation in annotations_query.yield_per(100):
             annotation_hit_histories_query = db.session.query(AppAnnotationHitHistory).filter(
@@ -460,6 +465,12 @@ class AppAnnotationService:
             for annotation_hit_history in annotation_hit_histories_query.yield_per(100):
                 db.session.delete(annotation_hit_history)
 
+            # if annotation reply is enabled, delete annotation index
+            if app_annotation_setting:
+                delete_annotation_index_task.delay(
+                    annotation.id, app_id, current_user.current_tenant_id, app_annotation_setting.collection_binding_id
+                )
+
             db.session.delete(annotation)
 
         db.session.commit()