diff --git a/modelscope/hub/api.py b/modelscope/hub/api.py
index 00254f16..eacde64a 100644
--- a/modelscope/hub/api.py
+++ b/modelscope/hub/api.py
@@ -266,6 +266,14 @@ class HubApi:
                 logger.info('Create new branch %s' % revision)
                 git_wrapper.new_branch(tmp_dir, revision)
             git_wrapper.checkout(tmp_dir, revision)
+            files_in_repo = os.listdir(tmp_dir)
+            for f in files_in_repo:
+                if f[0] != '.':
+                    src = os.path.join(tmp_dir, f)
+                    if os.path.isfile(src):
+                        os.remove(src)
+                    else:
+                        shutil.rmtree(src, ignore_errors=True)
             for f in files_to_save:
                 if f[0] != '.':
                     src = os.path.join(model_dir, f)
diff --git a/tests/hub/test_hub_upload.py b/tests/hub/test_hub_upload.py
index e1f61467..835aa62b 100644
--- a/tests/hub/test_hub_upload.py
+++ b/tests/hub/test_hub_upload.py
@@ -7,7 +7,7 @@ import uuid
 
 from modelscope.hub.api import HubApi
 from modelscope.hub.constants import Licenses, ModelVisibility
-from modelscope.hub.errors import HTTPError, NotLoginException
+from modelscope.hub.errors import GitError, HTTPError, NotLoginException
 from modelscope.hub.repository import Repository
 from modelscope.utils.constant import ModelFile
 from modelscope.utils.logger import get_logger
@@ -97,6 +97,17 @@ class HubUploadTest(unittest.TestCase):
             revision='new_revision/version1')
         assert os.path.exists(os.path.join(add4_path, 'add4.py'))
         shutil.rmtree(self.repo_path, ignore_errors=True)
+        assert os.path.exists(os.path.join(self.finetune_path, 'add3.py'))
+        os.remove(os.path.join(self.finetune_path, 'add3.py'))
+        self.api.push_model(
+            model_id=self.create_model_name,
+            model_dir=self.finetune_path,
+            revision='new_revision/version1')
+        Repository(
+            model_dir=self.repo_path,
+            clone_from=self.create_model_name,
+            revision='new_revision/version1')
+        assert not os.path.exists(os.path.join(self.repo_path, 'add3.py'))
 
     @unittest.skipUnless(test_level() >= 0, 'skip test in current test level')
     def test_upload_non_exists_repo(self):
@@ -133,7 +144,7 @@ class HubUploadTest(unittest.TestCase):
     def test_upload_invalid_repo(self):
         logger.info('test upload to invalid repo!')
         self.api.login(TEST_ACCESS_TOKEN1)
-        with self.assertRaises(HTTPError):
+        with self.assertRaises((HTTPError, GitError)):
             self.api.push_model(
                 model_id='%s/%s' % ('speech_tts', 'invalid_model_test'),
                 model_dir=self.finetune_path,