A new method of waveform reconstruction based on neural network is proposed to solve the problem of nano-second pulse distortion, which is caused by the existence of parasitic parameters and insufficient bandwidth in high-speed digital acquisition channels. The local mapping relationship between the distortion waveform acquired by the high-speed digital acquisition system and the reference waveform obtained from the oscilloscope is identified through single neural networks. Then, the global waveform is reconstructed by a series of neural networks. The experimental results show that the proposed method can obviously alleviate the problems such as the edge delay, overshoot of the distortion waveform, thus it can improve the power estimation accuracy by 32.5%, as well as improve the frequency response characteristics of the high-speed digital acquisition system.