The present disclosure discloses a method for controlling a standing wave accelerator and a system thereof. The method comprises: generating, by an electron gun, an electron beam; injecting the electron beam into an accelerating tube; and controlling a microwave power source to generate and input microwave with different frequencies into the accelerating tube, so that the accelerating tube switches between different resonant modes at a predetermined frequency to generate electron beams with corresponding energy. According to the above solution, it only needs to change the output frequency of the microwave power source in the process of adjusting energy, without making any change to the accelerating structure per se. Therefore, the method is easy to operate. In addition, the structure of the accelerating tube in the above system is simple, without adding a particular regulation apparatus.