diff --git a/api/extensions/ext_storage.py b/api/extensions/ext_storage.py
index a609f13dbc..6df0879694 100644
--- a/api/extensions/ext_storage.py
+++ b/api/extensions/ext_storage.py
@@ -112,7 +112,7 @@ class Storage:
     def exists(self, filename):
         return self.storage_runner.exists(filename)
 
-    def delete(self, filename):
+    def delete(self, filename: str):
         return self.storage_runner.delete(filename)
 
     def scan(self, path: str, files: bool = True, directories: bool = False) -> list[str]:
diff --git a/api/services/file_service.py b/api/services/file_service.py
index b0c5a32c9f..1980cd8d59 100644
--- a/api/services/file_service.py
+++ b/api/services/file_service.py
@@ -3,8 +3,8 @@ import os
 import uuid
 from typing import Literal, Union
 
-from sqlalchemy import Engine
-from sqlalchemy.orm import sessionmaker
+from sqlalchemy import Engine, select
+from sqlalchemy.orm import Session, sessionmaker
 from werkzeug.exceptions import NotFound
 
 from configs import dify_config
@@ -29,7 +29,7 @@ PREVIEW_WORDS_LIMIT = 3000
 
 
 class FileService:
-    _session_maker: sessionmaker
+    _session_maker: sessionmaker[Session]
 
     def __init__(self, session_factory: sessionmaker | Engine | None = None):
         if isinstance(session_factory, Engine):
@@ -236,11 +236,10 @@ class FileService:
         return content.decode("utf-8")
 
     def delete_file(self, file_id: str):
-        with self._session_maker(expire_on_commit=False) as session:
-            upload_file: UploadFile | None = session.query(UploadFile).where(UploadFile.id == file_id).first()
+        with self._session_maker() as session, session.begin():
+            upload_file = session.scalar(select(UploadFile).where(UploadFile.id == file_id))
 
-        if not upload_file:
-            return
-        storage.delete(upload_file.key)
-        session.delete(upload_file)
-        session.commit()
+            if not upload_file:
+                return
+            storage.delete(upload_file.key)
+            session.delete(upload_file)