The invention provides a multi-CPU current transformer synchronization control system based on a VME (versa module eurocard) bus and a synchronization method thereof. The control system comprises a main CPU and a plurality of secondary CPUs. The main CPU and the secondary CPUs are connected through the VME bus. The control system also comprises a clock signal generation circuit which is connected with the main CPU and the secondary CPUs respectively. The clock signal generation circuit generates a fixed common clock signal and triggers external interruption processing tasks of the main CPU and the secondary CPUs, counters of the main CPU and the secondary CPUs are cleared, counting is started again, and synchronous execution of the external interruption processing tasks of the main CPU and the secondary CPUs is realized. According to the system and the method in the invention, control performance of the control system is substantially raised, and reliability and security of system operation are enhanced.