A detailed structural model of the crust, subducting slab, and underlying upper mantle across the northern Izu-Ogasawara (Bonin) island are system is derived from a marine seismic reflection and ocean bottom seismographic refraction survey and subsequent forward modeling combined with tomographic inversion. The model indicates that the crust is thickest beneath the presently active rift zone and a granitic crust may have formed in the mid-crust. A highly attenuative mantle (that is, one with low quality Q) seems to be confined mainly beneath the presently active rift zone. In contrast, high P-wave velocity persists in the lower crust between the forearc and eastern margin of the back are basin, suggesting a large-scale magma input responsible for the are formation.