The invention relates to a fuel cell system and a control method thereof. The system comprises a galvanic pile, a hydrogen loop, an air loop, a cooling loop, a control module and an environment monitoring module, the hydrogen loop, the air loop and the cooling loop are all connected with the galvanic pile, and the control module receives information of each loop and the environment monitoring module, and regulates and controls each loop through calculation; the air loop comprises an air inlet pipeline, an air compressor, a cathode flow control module, a humidifier, a throttle valve and an exhaust pipeline, the air inlet pipeline, the air compressor, the humidifier and the inlet end of the galvanic pile are sequentially connected through pipelines, and the outlet end of the galvanic pile issequentially communicated with the humidifier, the throttle valve and the exhaust pipeline. And the cooling loop comprises a second pressure controller, a heater, a multi-module heat dissipation module and a flow control module. The defects in a common fuel cell are overcome, and the adaptive capacity of the system for different environments is improved.