The present invention provides a fuel cell hybrid power system and a control method thereof. The system includes a low temperature type fuel cell stack, a secondary battery pack, a motor unit, a transmission mechanism and a control unit. The motor unit is electrically connected to the low temperature type fuel cell stack and the secondary battery pack. The transmission mechanism is mechanically connected to the motor unit, so that the motor unit selectively outputs a power via the transmission mechanism. The low-temperature fuel cell stack is electrically connected to the secondary battery pack. The control unit is connected to the low temperature type fuel cell stack, the secondary battery pack, the motor unit and the transmission mechanism. The low-temperature fuel cell stack and the secondary battery pack drive the motor unit and the transmission mechanism alternately or integrally according to different demands. When the transmission mechanism deceleration or brakes, the low-temperature type fuel cell stack charges the secondary battery pack. The invention can improve the operation stability of different driving modes, simplify the structure and improve the usage efficiency of waste heat.