A backup system and a backup method thereof are provided. The backup system includes an operational storage, a backup storage, a service client, a metadata server and a backup client. The service client accesses the operational storage according to an operational storage layout metadata and makes a data change to the operational storage to transmit a metadata update request. The metadata server receives the metadata update request from the service client, updates a local operational storage layout metadata in response to the data change according to the metadata update request, acknowledges the metadata update request and instructs the backup client to back up the data change of the operational storage to the backup storage according to the metadata update request.