The invention discloses an auxiliary power unit (APU) controlling method for a gas-electric hybrid system. In a series-connection high-speed generation mode and in a rotating speed tracking mode of a vehicle, an integrated starter generator (ISG) is controlled by rotating speed, and an engine is controlled by a throttle; in the series-connection high-speed generation mode, the target rotating speed of the ISG is the rotating speed for generation, and the throttle valve of the engine is preset; in the rotating speed tracking mode, the target rotating speed of the ISG is the current rotating speed of a main motor, and the throttle valve of the engine is zero. According to the APU controlling method for the gas-electric hybrid system, in the series-connection high-speed generation mode and in the rotating speed tracking mode, the ISG is controlled by rotating speed, speed adjusting response is quick especially during climbing, the hybrid system can quickly switch into the series-connection mode, then the engine and the main motor provide power at the same time, and the dynamic property of the vehicle is excellent; and during high-speed generation at the preset rotating speed, the ISG is controlled by rotating speed, and the engine is controlled by the preset throttle, so that up-down fluctuation of the rotating speed of the engine can be reduced, and generation efficiency is improved.