The Ryukyu arc (RA)-trough system is uniquely characterized by an active back-arc basin of the Okinawa Trough (OT), extending ∼1,000 km from the southwest of Kyushu, Japan to the east of Taiwan with extensive active rifting (Sibuet et al., 1998) (Figure 1). The OT, bounded by the East China Sea (ECS) continental shelf in the west and the RA in the east, is divided by the Tokara channel and the Kerama gap with large bathymetric depressions across the RA into three parts: north, middle and south (Figure 1). The rifting rates along the OT progressively increase from ∼23 mm/year in the north to ∼46 mm/year in the south, which correlates with the gradually increasing convergence rates along the Ryukyu subduction zone from ∼80 mm/year to ∼122 mm/year toward the south (Arai et al., 2017; Argus et al., 2011). The OT, which has been undergoing an early stage of continental disintegration, provides a unique location to study the lithospheric evolution in an extensional regime at the continental margin as well as the interaction with the arc activity. Thus, a good image of the crustal structure is crucial to understanding the regional tectonics of the RA-trough system and how continental rifting evolves in general.