We applied tomographic inversion and receiver function analysis to seismic data from ocean-bottom seismometers and land-based stations to understand the structure and its relationship with slow slip events off Boso, Japan. First, we delineated the upper boundary of the Philippine Sea Plate based on both the velocity structure and the locations of the low-angle thrust-faulting earthquakes. The upper boundary of the Philippine Sea Plate is distorted upward by a few kilometers between 140.5 and 141.0°E. We also determined the eastern edge of the Philippine Sea Plate based on the delineated upper boundary and the results of the receiver function analysis. The eastern edge has a northwest–southeast trend between the triple junction and 141.6°E, which changes to a north–south trend north of 34.7°N. The change in the subduction direction at 1–3 Ma might have resulted in the inflection of the eastern edge of the subducted Philippine Sea Plate. Second, we compared the subduction zone structure and hypocenter locations and the area of the Boso slow slip events. Most of the low-angle thrust-faulting earthquakes identified in this study occurred outside the areas of recurrent Boso slow slip events, which indicates that the slow slip area and regular low-angle thrust earthquakes are spatially separated in the offshore area. In addition, the slow slip areas are located only at the contact zone between the crustal parts of the North American Plate and the subducting Philippine Sea Plate. The localization of the slow slip events in the crust–crust contact zone off Boso is examined for the first time in this study. Finally, we detected a relatively low-velocity region in the mantle of the Philippine Sea Plate. The low-velocity mantle can be interpreted as serpentinized peridotite, which is also found in the Philippine Sea Plate prior to subduction. The serpentinized peridotite zone remains after the subduction of the Philippine Sea Plate and is likely distributed over a wide area along the subducted slab.