For the waveform distortion of narrow pulse signal after amplification, frequency conversion and other analog devices, a waveform distortion correction method for signals based on modified frequency domain filter is proposed. Traditional distortion correction methods only use signals within the effective bandwidth. It results in poor time domain performance after waveform distortion correction. To improve the distortion correction accuracy and ensure the time domain waveform characteristics of the signal, the proposed method uses the frequency responses of the effective bandwidth and the partial high-frequency region outside the bandwidth to solve the waveform distortion correction filter. But the spectrum of the distortion correction filter fluctuates greatly and has many spikes and burrs in the high-frequency region outside the bandwidth. It can′t be directly used to solve the coefficients of the waveform distortion correction filter. The proposed method applies median filtering to the amplitude-frequency response correction curves and phase-frequency response correction curves, followed by polynomial fitting. Better waveform correction performance has been achieved by optimizing the order and coefficients of the waveform distortion correction filter. Finally, the real data processing results verified the effectiveness of the proposed method.