Crustal structures around the Yamato Basin in the southeastern Sea of Japan, inferred from recent ocean bottom seismography (OBS) and active‐source seismological studies, are reviewed to elucidate various stages of crustal modification involved from rifting in the crust of the surrounding continental arc to the production of oceanic crust in the Yamato Basin of the back‐arc basin. The northern, central, and southern areas of the Yamato Basin have crustal thicknesses of approximately 12–16 km, and lowermost crusts with P‐wave velocities greater than 7.2 km/s. Very few units have P‐wave velocities in the range 5.4–6.0 km/s, which corresponds to the continental upper crust. These findings, combined with previous geochemical analysis of basalt samples, are interpreted to indicate that a thick oceanic crust has been formed in these areas of the basin, and that this oceanic crust has been underplated by mantle‐derived magma. In the central Yamato Basin, the original continental crust has been fully breached and oceanic crust has been formed. Conversely, the presence of a unit corresponding to the continental upper crust and the absence of a high‐velocity part in the lower crust implies that the southwestern edge of the Yamato Basin has a rifted crust without significant intrusion. The Oki Trough has a crust that is 17–19 km thick with a high‐velocity lower crust and a unit corresponding to the continental upper crust. The formation of the Oki Trough resulted from rifting with magmatic intrusion and/or underplating. We interpret these variations in the crustal characteristics of the Yamato Basin area as reflecting various instances of crustal modification by thinning and magmatic intrusion due to back‐arc extension, resulting in the production of a thick oceanic crust in the basin.