Slip on the shallow part of a megasplay fault that is an out-of-sequence thrust and branch of the main subduction plate boundary can cause devastating tsunamis after earthquakes. We analyzed the three-dimensional geometry, including dip amount and azimuths, roughness distributions, and thickness variations, of the shallow part of a megasplay fault in the Nankai Trough using a three-dimensional seismic data set. The fault is divided into three zones based on its geometry: thick, smooth, and simply convex in the east; complexly curved in the middle; and thin and kinked in the west. Results of scientific drilling indicate that the eastern region of the fault is most active, and local heterogeneities in fault geometry, including roughness and thickness, may control the slip on this part of the fault. The present findings can be used to evaluate the risk of future tsunamis arising from movement on shallow thrust faults at subduction margins.