Typhoons play a significant role in the marine sedimentary dynamic process and thus could significantly change the submarine geomorphology in their influence area. In this study, a high-resolution sub-bottom profiler and a side-scan sonar were used to detect the submarine geomorphology of the southeast coastal area of Nanri Island in the Taiwan Strait before and after Typhoon Soudelor—three times in 2015. The results show that the typhoon induced seaward movement of the sand dunes up to several tens of meters, resulting in significant changes in both the shape of the sand dunes and the scale of the exposed bedrocks. The typhoon also changed the submarine geomorphology, including the smoothing of anchor traces of fishing boats and the formation of relatively small sand dunes (groups). A comparison of the results of different surveys shows that the submarine geomorphology that was changed by Typhoon Soudelor could not recover within a short period of time. The wind field simulations of the typhoon process showed that the storm wave caused by the strong wind stress of the typhoon was a key dynamic factor for changing the submarine geomorphology.