diff --git a/scripts/migrate-repo.py b/scripts/migrate-repo.py
index a4fd7328df..e1a4c9fdc5 100644
--- a/scripts/migrate-repo.py
+++ b/scripts/migrate-repo.py
@@ -4,6 +4,7 @@ import os
 import sys
 import logging
 import configparser 
+import json
 from sqlalchemy import create_engine, text
 from sqlalchemy.orm import sessionmaker
 from migrate import ObjMigrateWorker
@@ -29,7 +30,7 @@ def main(argv):
     else:
         migrate_repo(repo_id, orig_storage_id, dest_storage_id)
 
-def parse_seafile_config():
+def parse_seafile_config(storage_id):
     env = os.environ
     seafile_conf = os.path.join(env['SEAFILE_CENTRAL_CONF_DIR'], 'seafile.conf')
     cp = configparser.ConfigParser()
@@ -39,13 +40,33 @@ def parse_seafile_config():
     user = cp.get('database', 'user')
     passwd = cp.get('database', 'password')
     db_name = cp.get('database', 'db_name')
-    return host, port, user, passwd, db_name
 
-def get_repo_ids():
-    host, port, user, passwd, db_name = parse_seafile_config()
-    url = 'mysql+pymysql://' + user + ':' + passwd + '@' + host + ':' + port + '/' + db_name
-    print(url)
-    sql = 'SELECT repo_id FROM Repo'
+    is_default = is_default_storage(cp, storage_id)
+
+    return host, port, user, passwd, db_name, is_default
+
+def is_default_storage(cp, orig_storage_id):
+    json_file = cp.get('storage', 'storage_classes_file')
+    f = open(json_file)
+    json_cfg = json.load(f)
+
+    is_default = False
+
+    for bend in json_cfg:
+        storage_id = bend['storage_id']
+        if storage_id == orig_storage_id:
+            if 'is_default' in bend:
+                is_default = bend['is_default']
+                break
+
+    return is_default
+
+def get_repo_ids_by_storage_id (url, storage_id = None):
+    if storage_id:
+        sql = 'SELECT repo_id FROM RepoStorageId WHERE storage_id=\"%s\"'%(storage_id)
+    else:
+        sql = 'SELECT repo_id FROM RepoStorageId'
+
     try:
         engine = create_engine(url, echo=False)
         session = sessionmaker(engine)()
@@ -53,8 +74,52 @@ def get_repo_ids():
     except:
         return None
     else:
-        result = result_proxy.fetchall()
-    return result
+        results = result_proxy.fetchall()
+
+    repo_ids = {}
+    for r in results:
+        try:
+            repo_id = r[0]
+        except:
+            continue
+        repo_ids[repo_id] = repo_id
+    return repo_ids
+
+def get_repo_ids(storage_id):
+    host, port, user, passwd, db_name, is_default = parse_seafile_config(storage_id)
+    url = 'mysql+pymysql://' + user + ':' + passwd + '@' + host + ':' + port + '/' + db_name
+
+    if is_default:
+        all_repo_ids = get_repo_ids_by_storage_id (url)
+    storage_repo_ids =  get_repo_ids_by_storage_id (url, storage_id)
+
+    sql = 'SELECT repo_id FROM Repo'
+
+    try:
+        engine = create_engine(url, echo=False)
+        session = sessionmaker(engine)()
+        result_proxy = session.execute(text(sql))
+    except:
+        return None
+    else:
+        results = result_proxy.fetchall()
+
+    ret_repo_ids = []
+    for r in results:
+        try:
+            repo_id = r[0]
+        except:
+            continue
+        #If it's default storage, we should also return the repos which are not in the RepoStorageID table.
+        #Repo table is checked to preventing returning deleted repos.
+        if is_default:
+            if repo_id in storage_repo_ids or not repo_id in all_repo_ids:
+                ret_repo_ids.append(repo_id)
+        else:
+            if repo_id in storage_repo_ids:
+                ret_repo_ids.append(repo_id)
+
+    return ret_repo_ids
 
 def migrate_repo(repo_id, orig_storage_id, dest_storage_id):
     api.set_repo_status (repo_id, REPO_STATUS_READ_ONLY)
@@ -100,13 +165,9 @@ def migrate_repo(repo_id, orig_storage_id, dest_storage_id):
     logging.info('The process of migrating repo [%s] is over.\n', repo_id)
 
 def migrate_repos(orig_storage_id, dest_storage_id):
-    repo_ids = get_repo_ids()
+    repo_ids = get_repo_ids(orig_storage_id)
 
     for repo_id in repo_ids:
-        try:
-            repo_id = repo_id[0]
-        except:
-            continue
         api.set_repo_status (repo_id, REPO_STATUS_READ_ONLY)
         dtypes = ['commits', 'fs', 'blocks']
         workers = []