The existing waveform processing methods in the airborne Lidar bathymetry system are reviewed. Based on the multi-channel advantages of the domestic airborne Lidar bathymetry waveform data and by using the multiple waveform processing methods, such as deconvolution, numerical fitting and signal filtering, a set of waveform processing methods suitable for domestic hardwares is proposed as for different types of waveforms. This set of methods can ensure the robustness of waveform peak position extraction.