Tidal flats are internationally protected areas because of their environmental, geological, and economic value. Nevertheless, these are areas where casualties are common among visitors. To ensure the safety of visitors, efforts must be made to understand the geomorphologic characteristics of tidal flats. It is necessary to use three-dimensional topographic data to clearly determine when an exposed tidal flat rapidly disappears as a result of periodic tidal fluctuations. Digital elevation models (DEMs) created using unmanned aerial vehicle (UAV) imaging and commercial photogrammetric software to measure tidal flats are produced using ground control points (GCPs). It is difficult to conduct field surveys and readings of image coordinates that correspond to these because tidal flat areas are difficult to access. The distribution of GCPs affects the accuracy of a DEM because the entire test region cannot be covered during a survey. Without GCPs, the DEM generated with the UAV images and photogrammetric software using the structure from motion (SfM) technique probably has nonlinear distortion such as a bowl shape. This paper proposes a practical method of least-squares three-dimensional (3D) surface matching with a polynomial model (LS3D-PM) to correct a distorted DEM. For this LS3D-PM matching, a global TanDEM-X DEM was used instead of a field survey to collect the GCPs in a tidal flat. Practical testing was conducted using the proposed method. The root mean square error with respect to the height decreased from approximately 1.0 m to 0.1 m, and the bowl-effect error was eliminated. With the DEM corrected using the proposed method and the classified orthoimages, the exposed tidal flat changes due to seawater invasion were estimated at different times during flood tide. This method has non-trivial technical values for quick and relatively precise DEM generations at a low cost compared to that of other techniques, particularly in emergency situations such as tsunamis, landslides, and earthquakes.