Coastal tidal flat wetlands are valuable natural resources that provide diverse habitats and important ecological barriers. The physical environment of the intertidal zone poses many challenges to the monitoring of tidal flat topography, making it difficult to implement traditional measurement methods, and satellite remote sensing combined with tide level information makes it possible to invert coastal tidal flat topography more conveniently over large areas. Current methods based on inundation frequency fail to consider the effect of water level distribution of remote sensing images, and usually use all available remote sensing images. However, the uneven distribution of image tide levels will increase the error of the tidal flat construction. Therefore, in this study, according to the distribution characteristics of the water level in remote sensing images, we adaptively exclude the images with a concentrated water level distribution, so as to make the water level distribution more uniform, and thus reduce the topographic inversion error. The validation results of the inversion accuracy show that the root mean squared error of the tidal flat topographic inversion improved by about 5 cm compared with the previous inundation frequency method, which is suitable for reconstructing the tidal flat topography on a large scale and a long-time scale, and it can be used as a basis for coastal tidal flat protection and restoration decision making.