This paper presents a Compact Integrated Water–Land Survey System (CIWS), which combines a remote sensing camera and a LiDAR module, and proposes an innovative underwater topography retrieval technique based on this system. This technique utilizes high-precision water depth points obtained from LiDAR measurements as control points, and integrating them with the grayscale values from aerial photogrammetry images to construct a bathymetry retrieval model. This model can achieve large-scale bathymetric retrieval in shallow waters. Calibration of the UAV-mounted LiDAR system was conducted using laboratory and Dongjiang Bay marine calibration fields, with the results showing a laser depth measurement accuracy of up to 10 cm. Experimental tests near Miaowan Island demonstrated the generation of high-precision 3D seabed topographic maps for the South China Sea area using LiDAR depth data and remote sensing images. The study validates the feasibility and accuracy of this integrated scanning method for producing detailed 3D seabed topography models.