A rack server system and an operating method applicable thereto are provided. The rack server system includes a battery backup unit (BBU) and at least one server. The operating method includes: communicating the server and the BBU with each other; the BBU providing a status information and a previous self-discharging test information to the server for the server to judge a status of the BBU; and providing power from the BBU to the server and adjusting a loading of the server according to the status information of the BBU when an input power is interrupted.