Three large bathymetric highs (from north to south: the Amami Plateau, the Daito Ridge, and the Oki-Daito Ridge) originating from paleo-island arcs characterize the northwestern end of the Philippine Sea plate. We obtained 10 seismic refraction and multi-channel seismic reflection profiles across and along these bathymetric highs and obtained P wave velocity (Vp) models of the crust and the uppermost mantle. Although there are large variations in the crustal structure throughout this region, these bathymetric highs usually have a middle crust with Vp of 6.3 to 6.8 km/s, a lower crust with Vp of 6.8 to 7.2 km/s, a Pn velocity of 7.6 to 7.8 km/s, and a total crustal thickness of 15 to 25 km. These features are similar to those of the Izu-Ogasawara (Bonin)-Mariana island arc and the Kyushu-Palau Ridge, which are immature paleo-island arcs. However, the crust at the southwestern part of the Oki-Daito Ridge contains a relatively thin middle crust and a smaller total crustal thickness compared with other ridges in this region. In addition, we identified a deep reflector beneath the ridge, with these properties indicating a different origin, such as intraplate volcanism.