A rack server system and a control method thereof are provided. The rack server system establishes a communication link for communicating with a battery backup unit. The battery backup unit is connected to a power input port of the rack server system, and includes a number of battery modules connected with each other in parallel. The rack server system controls the battery backup unit to perform validity test on a first battery module during a first period and to perform validity test on a second battery module during a second period, wherein the first period and the second period are not overlapped with each other.