Slow earthquakes are crucial for understanding the nature of subducting plate boundaries and their seismic coupling. Although many very low-frequency earthquakes (VLFEs) have been recently recorded in the central part of the Nankai Trough, there have been only rare cases reported between the Kii Channel and Cape Shionomisaki. To investigate the structural features and their potential relationship with the slow events, in November 2018, JAMSTEC deployed a dense array of 96 ocean-bottom seismometers (OBS) to acquire an active-source seismic refraction dataset from the seaward side of the subduction trough to the accretionary prism off Cape Shionomisaki. We applied travel time and waveform tomography to the OBS data and reconstructed the seismic P-wave velocity model down to the upper mantle. The subsurface velocity model reveals some new discovered features, and describes the accretionary prism as consisting of a weak outer wedge and a strong inner wedge. The velocity anomaly bodies inside the wedge possibly link to specific deformation processes and the evolution of the accretionary prism. As compared to a transect across the adjacent Kumano Basin, where there are densely distributed VLFEs, the distinct results from these two locations reveal potential structural and physical differences that cause variability in seismic activities.