Abstract We performed 3D seismic tomography of the Hyuga-nada region, western Nankai subduction zone, to investigate the relationship of the subducted part of Kyushu-Palau Ridge (KPR) to coseismic rupture propagation, seismicity, and shallow very low frequency earthquakes. Combining active-source and passive-source data recorded both onshore and offshore, we imaged the deep slab from near the trough axis to the coastal area. Our results show the subducted KPR as a low-velocity belt oriented NW–SE extending down the plate boundary to around 30 km depth. At this depth, we suggest that the subducted KPR detaches from the slab and becomes underplated on the overriding continental plate. As the coseismic slip areas of past large earthquakes do not extend into the subducted KPR, we suggest that it may inhibit rupture propagation. The interior of the subducted KPR shows active intraslab seismicity with a wide depth distribution. Shallow very low frequency earthquakes are continuously active above the location of the subducted KPR, whereas they are intermittent to the northeast of the subducted KPR. Thus, the subducted KPR appears to be an important factor in coseismic rupture propagation and seismic phenomena in this region.