The invention provides an on-line testing method and system for the microwave amplifier irradiation effect. The method comprises the steps that the indicators of a microwave amplifier to be tested are tested; after the test is passed, a master control chassis controls a front probe to power the microwave amplifier to be tested and provide an excitation signal source before, during and after irradiation of the microwave amplifier; and the front probe is used to measure the output signal power of the microwave amplifier to be tested and outputs the power. According to the invention, the front probe is arranged to measure the frequency range, small signal gain, saturation power, efficiency and other technical indicators of the microwave amplifier; the use requirement of the microwave amplifier is met; and the on-line testing method and system are practical.