Efficiently and quickly measuring shallow waters, islands, reefs, ledges and unreachable waters for ships, an airborne bathymetric LiDAR system is able to measure deep to 50 meters, covering the entire inshore region, while the ship-based mobile measurement system is capable of obtaining topographic data of the ocean floor in inshore shallow sea and fine 3D laser point cloud of islands and reefs. These systems have some complementarity in the area and range of measurement. In this paper, an improved iterative closest point (ICP) algorithm based on feature points of curvature is applied to conduct registration and fusion of airborne bathymetric data, multi-beam data and 3D laser scanning data obtained from the domestic airborne bathymetric LiDAR system and the ship-based mobile measurement system, as well as comprehensively and accurately describe the terrain of both coastal waters and inshore areas for a unified criterion. The results show that the registration data from the airborne bathymetric LiDAR system and the ship-based mobile measurement system can be of great significance in comprehending the topography of islands and reefs, as well as detecting and discovering underwater targets.