The complex and changing underwater environment, along with the presence of various suspended particles, leads to laser attenuation and backward scattering. As a result, the detection capabilities of underwater LiDAR are significantly limited. To address the challenges associated with the backward scattering problem using traditional time discrimination circuits, this paper proposes a high-speed signal processing system for underwater LiDAR based on complete waveform sampling. The system includes the design of a photodiode preamplifier circuit and a main control board with a sampling frequency of up to 2 GHz. With this design, the underwater LiDAR can achieve a ranging accuracy of 0.075m and implement relevant backscatter filtering algorithms. This paper can serve as a valuable reference for the design of signal processing systems for underwater LiDAR