diff --git a/download-deps.py b/download-deps.py
index 562a5183e3..edf239cdfd 100755
--- a/download-deps.py
+++ b/download-deps.py
@@ -51,9 +51,22 @@ from sys import stdout
 from distutils.errors import DistutilsError
 from distutils.dir_util import copy_tree, remove_tree
 
-def execute_command(cmd):
-    if os.system(cmd) != 0:
-        raise Exception('Command ( %s ) failed!' % cmd)
+
+def delete_folder_except(folder_path, excepts):
+    """
+    Delete a folder excepts some files/subfolders, `excepts` doesn't recursively which means it can not include
+    `subfoler/file1`. `excepts` is an array.
+    """
+    for file in os.listdir(folder_path):
+        if (file in excepts):
+            continue
+
+        full_path = os.path.join(folder_path, file)
+        if os.path.isdir(full_path):
+            shutil.rmtree(full_path)
+        else:
+            os.remove(full_path)
+
 
 class UnrecognizedFormat:
     def __init__(self, prompt):
@@ -242,9 +255,10 @@ class CocosZipInstaller(object):
             data = json.load(data_file)
         return data
 
-    def clean_external_folder(self):
+    def clean_external_folder(self, external_folder):
         print('==> Cleaning cocos2d-x/external folder ...')
-        execute_command('git clean -fdx external')
+        # remove external except 'config.json'
+        delete_folder_except(external_folder, ['config.json'])
 
     def run(self, workpath, folder_for_extracting, remove_downloaded, force_update, download_only):
         if not force_update and not self.need_to_update():
@@ -262,7 +276,7 @@ class CocosZipInstaller(object):
             if not os.path.exists(folder_for_extracting):
                 os.mkdir(folder_for_extracting)
 
-            self.clean_external_folder()
+            self.clean_external_folder(folder_for_extracting)
             print("==> Copying files...")
             distutils.dir_util.copy_tree(self._extracted_folder_name, folder_for_extracting)
             if self._move_dirs is not None: