The invention discloses a digital pileup waveform processing method and a digital pileup waveform processing system. The method comprises the following steps of: determining a pulse rising edge area, and judging whether a pulse has a pileup waveform or not according to a time interval between adjacent pulse rising edges; and dividing a digital waveform determined as pileup according to the risingedge and the falling edge of the pulse, reconstructing single event pulse waveforms in turn by using the divided waveform, and extracting single pulse information from the reconstructed waveforms. The invention also discloses the pileup waveform processing system, which comprises a pileup waveform discrimination module, a pulse waveform division module and a pulse waveform reconstruction module. By the method and the system, the pileup pulse waveform can be effectively discriminated, each single event pulse waveform in the pileup is accurately reconstructed, information such as energy, time, amplitude, decay time constant, position and the like of the single event pulse is accurately recovered, and the counting rate of a system under high activity, and the signal-to-noise ratio of a measuring result are improved.