Abstract: An identification method of seabed weak echoes in airborne LiDAR bathymetry and a system thereof are provided, which belong to the technical field of marine surveying and mapping. The method includes: dividing sea area laser pulses into surface-seabed pulses or seabed-undefined pulses based on preprocessed data; using two-stage local maximum method to determine potential seabed echo positions of ALB waveforms and pre-generate seabed points; defining an ellipsoid neighborhood related to density and extracting spatial features of a pre-generated point cloud; constructing a BP neural network to identify seabed points in the pre-generated point cloud, and optimizing the identification result of the seabed points based on a laser pulse echo sequence and point cloud density.