The invention relates to a shutdown purging system and a purging method for a vehicle-mounted fuel cell power generation system. The system comprises a fuel cell, a vehicle control unit, a fuel cell controller, a power output relay, an air pump, a hydrogen tail exhaust electromagnetic valve, a fuel cell temperature acquisition device and an environmental temperature acquisition device. A control method comprises the step that the fuel cell controller controls the rotating speed of the air pump, the exhaust period of the hydrogen tail exhaust electromagnetic valve and the purging time in the shutdown process according to the temperature of the fuel cell and the environmental temperature. The shutdown purging system and the purging method for the vehicle-mounted fuel cell power generation system have the beneficial effects that the purging process depends on power generated by the fuel cell power generation system and the feed of a storage battery, which is caused by shutdown purging, can be prevented; and the purging is not limited by time, is determined according to the fuel cell and the environment state and is completely carried out by liquid water.