Side-scan sonar (SSS) is used for obtaining high-resolution seabed images, but with low position accuracy without using the Ultra Short Base Line (USBL) or Short Base Line (SBL). Multibeam echo sounder (MBES), which can simultaneously obtain high-accuracy seabed topography as well as seabed images with low resolution in deep water. Based on the complementarity of SSS and MBES data, this paper proposes a new method for acquiring high-resolution seabed topography and surface details that are difficult to obtain using MBES or SSS alone. Firstly, according to the common seabed features presented in both images, the Speeded-Up Robust Features (SURF) algorithm, with the constraint of image geographic coordinates, is adopted for initial image matching. Secondly, to further improve the matching performance, a template matching strategy using the dense local self-similarity (DLSS) descriptor is adopted according to the self-similarities within these two images. Next, the random sample consensus (RANSAC) algorithm is used for removing the mismatches and the SSS backscatter image geographic coordinates are rectified by the transformation model established based on the correct matched points. Finally, the superimposition of this rectified SSS backscatter image on MBES seabed topography is performed and the high-resolution and high-accuracy seabed topography and surface details can be obtained.