The Izu-Bonin arc (IBA) has been colliding with the Honshu arc since the middle Miocene, which together form the active Izu arc-arc collision zone (ICZ) in central Japan. To understand the entire collisional system, we have used refraction/wide-angle reflection data to model velocity structures of the Honshu arc, northwest of the ICZ. The seismic data indicate that the upper 4-km crust of the Honshu arc consists of a horizontally homogenous layer with P wave velocity (Vp) of 5.6 to 6.0 km/s and S wave velocity (Vs) of 3.4 to 3.7 km/s. This uniformity is in contrast with the heterogeneous structure further south, where the accreted crustal blocks of the IBA are bounded by dipping collisional boundaries. These contrasting structures suggest that crustal shorting caused by the arc-arc collision has been mostly accommodated within the IBA by reverse faulting along collisional boundaries, with the Honshu arc undergoing relatively little crustal deformation. The high-velocity body of the Kofu granitic complex (KGC), generated by partial melting of the subducted IBA crust, is mostly situated at >4-km depths but shallows significantly just beneath the Kofu Basin. This structural change implies that most of the KGC magma had erupted from just beneath the Kofu Basin.