The invention relates to a refrigerator vehicle fuel cell cooling system and a control method thereof. The refrigerator vehicle is provided with a liquid nitrogen refrigeration system. The liquid nitrogen refrigeration system comprises a liquid nitrogen tank, a valve box and a first evaporator. A fuel cell comprises a pile. The cooling system comprises a heat exchange device, an electronic water pump and a controller. The primary side input port of the heat exchange device is connected with the coolant outlet of the pile through a third pipeline. The primary side outlet of the heat exchange device is connected with the coolant inlet of the pile through a fourth pipeline. The secondary side input port of the heat exchange device is connected with the output end of the valve box through a fifth pipeline. A third solenoid valve is arranged on the fifth pipeline. The secondary side output port of the heat exchange device is connected with a second exhaust pipeline. The electronic water pump is arranged on the fourth pipeline. The controller is connected with a first solenoid valve, a second solenoid valve and the third solenoid valve. The cooling system has the advantages of compact structure, flexible control, strong adaptability and high cooling efficiency. The control method has the advantages of simple process, high execution efficiency, safety and reliability.