Along the western Nankai trough, southwest Japan, heterogeneous crustal structures, such as scattered deep strong reflectors and a subducted topographic high, showed a spatial relationship to along-trough variation in the coseismic slip during the 1946 Nankai earthquake, which is the most recent of repeated interplate earthquakes of magnitude 8 range in this area. We observed micro earthquakes using a temporary ocean bottom seismograph network off Shikoku Island, western Nankai trough. Near the trough axis off Cape Muroto, earthquakes in the subducting oceanic plate were associated with structures in the oceanic crust and the uppermost mantle of the subducting plate. Beneath the trough landward slope, the observed earthquakes suggest heterogeneous interplate coupling related to the crustal structure variations. The crustal structure variations could affect the interplate coupling during the interseismic period as well as coseismic rupture propagation during large interplate earthquakes along the western Nankai trough.