We carried out a reflection/refraction seismic survey across the southern Izu-Ogasawara arc–back arc system, covering three arcs with different crustal ages. The oldest Eocene arc has middle and lower crust with high velocities of 6.4–6.6 and 6.8–7.4 km/s, respectively, suggesting denser crustal materials. The current volcanic arc has middle and lower crust with lower velocities of 5.7–6.5 and 6.7–7.1 km/s, suggesting advanced crustal differentiation. The crust-mantle transition layer, with a velocity of 7.5–8.0 km/s, is distributed beneath the current volcanic arc and the rear arc, suggesting a pool of dense materials emanating from the crust through the crustal growth. These structural differences between the Eocene arc and current arc indicate a difference of crustal growth based on basaltic and andesitic magmas according to known petrologic studies. Commonly, rifted crusts have lower crusts with high velocities of over 7.0 km/s, and the arc–back arc transition zone also has a thinner more reflective crust that may have been affected by postrifting magmatism.