The results of a controlled source seismic reflection–refraction experiment carried out in 1992 reveal the following characteristics of the northern Izu–Bonin (Ogasawara) oceanic island arc–trench system. (1) The crust rapidly thickens from the Shikoku back‐arc basin to the arc, is thickest beneath the active rifts, and then gradually thins to the forearc. The thickness of the crust beneath the arc rift zone and the back‐arc basin are ∼ 20 km and 8 km, respectively. (2) The Moho vanishes beneath the forearc. Velocities rapidly decrease eastwards beneath the inner trench wall. (3) The velocity of the lower crust of the arc and the back‐arc basin is 7.1–7.3 km/s. This velocity is higher than the typical oceanic lower crust whose velocity is ∼ 6.7 km/s. (4) The velocity of the middle crust of the arc is ∼ 6 km/s. This layer does not exist beneath the back‐arc basin. (5) A slight difference in the velocity gradient of the middle crust exists between the arc rift zone and the forearc. Based on these findings and previous studies, it is inferred that: (i) the middle crust is probably granitic rock and formed in more than two episodes; (ii) the lower crust formed by igneous underplating which may also have affected part of the back‐arc basin; and (iii) the root of the serpentinite diapir on the inner trench wall is a low‐velocity mantle wedge that was probably caused by large amounts of water released from the subducting Pacific plate at depths shallower than 30 km.