The invention provides an X-ray pulse detection system signal processing method. The method performs high-frequency sampling and quantification of a pulse signal output by a detector, and performs threshold filtering and peak value detection so as to obtain accurate pulse amplitude information, wherein a threshold value in the threshold filtering can be tested according to star calibration and can be adjusted online in real time. The filtering method may effectively reduce an influence of noise on X-ray pulse detection so as to obtain accurate amplitude information of an X-ray pulse signal. Further, a local crystal oscillator records local sampling time, counts received atomic clock pulses, and records GPS time. A processing module may correct the local sampling time by using the counted atomic clock pulses so as to solve a problem of clock drifting of a detection system. As a result, the processing module may achieve X-ray pulse signal detection according to a result output by the method.