Abstract: Oyster reefs is an important coastal morphological system, the spatial distribution pattern of the reefs profoundly influences the surrounding hydrodynamic and sedimentary processes, which in turn affects the evolution of oyster reefs. The Liyashan oyster reef in Haimen, Jiangsu, is an important and rare ecosystem in the Chinese coast; however, it has been seriously degraded by sediment cover and human fishing in recent years. A geomorphological observation of the oyster reefs in Liyashan was carried out using an unmanned aerial vehicle (UAV). Based on the SfM (Structure from Motion) photogrammetry, high-resolution three-dimensional models of the aerial photography region were reconstructed, including orthophoto and digital elevation model (DEM). Then, the visual interpretation and profile analysis on the reconstructed models were conducted. Results show that the oyster reefs are mainly composed of three types in distribution shape: string, patch, and ring. The “string” oyster reef ridges are generally oriented north-south, likely were formed by the degradation of “ring” reefs or self-organization process of oysters. The elevation differences within the surveyed area could reach more than 5 m, the highest elevation was 0.5 m (1985 national elevation), while the lowest elevation was −4.7 m. The reefs are still in a degraded state, and the evolutionary process is mainly as follows: potholes appear on the surfaces of the reefs → further expansion and extension of potholes → formation of grooves→ segmentation and disintegration of the reefs, accompanied by sedimentary burial of the reefs. This study shows that the UAV SfM technique can efficiently obtain geomorphological data of oyster reefs, which provides a strong support for studying the evolution of oyster reefs.