To accurately estimate the coseismic rupture area in a Nankai megathrust earthquake and predict seismic and tsunami hazards, various three-dimensional models of the subducting plate geometry and simple seismic velocity models of the subduction zone in SW Japan have been proposed. However, to ensure consistency among studies, more realistic and reliable standard models must be developed. Here, we use wide-angle ocean-bottom seismographic survey results to develop models of the three-dimensional geometry of the subducting plate and of the three-dimensional P-wave velocity structure around the Nankai Trough. We confirmed the reliability of the proposed models by comparing theoretical first arrivals, calculated from two-dimensional structure models sampled from the three-dimensional model along seismic profile lines, with observed traveltime data. The proposed models are the first to be visible and to attempt to represent the actual seismic velocity structures around the entire Nankai Trough in SW Japan. Although the spatial validity of the three-dimensional velocity structure model could not be strictly evaluated, we confirmed that the differences between hypocenter parameters determined from previously published seismic tomography results and those obtained by using our three-dimensional structure model were sufficiently small (latitude and longitude within ±0.1° and depth within approximately ±5 km). Therefore, our three-dimensional structure model is suitable for use as an initial model for hypocenter determination.