The present disclosure relates to a lightweight and small bathymetry LiDAR multi-channel high sampling rate high-precision real-time synchronous acquisition and storage system, which adopts an ADC+FPGA+ZYNQ architecture to implement four-channel high-rate real-time synchronous parallel sampling, has synchronization error less than 300 ps, sampling rate s as high as 2 GSPS, and sampling precision as high as 14 bits, and comprises an FPGA system acquisition carrier board unit for implementing laser radar echo data acquisition and storage, PMT controlling, data maximum value feedback, peripheral interface design and storage control; a storage daughter board unit for implementing storage of echo data and export of 100 Mbps Ethernet, and an upper computer data conversion software for implementing conversion of original echo data files into decimal or hexadecimal csv files. The system has multi-channel parallel acquisition, high sampling rate and precision, strong real-time performance and functional applicability, and light weight and portability for bathymetry LiDAR.