We investigate the crustal structure of the NE South China Sea (SCS) margin to constrain its crustal thickness and basement nature with implications for the Mesozoic and Cenozoic evolution of the SCS. First-order interfaces interpreted from seismic reflection data were integrated into a 3D gravity inversion scheme to determine Moho depth and crustal thickness variations. A joint inversion of seismic and gravity data allowed us to determine crustal density variations along 2D profiles. The distal margin is divided into two distinct crustal domains: the Southern Rift System (SRS), and Southern High (SH). The SRS shows an extremely thinned continental crust on top of which thick Cenozoic sequences are observed. It is separated from the oceanic crust (~ 6 to 8 km thick) by the SH, a comparatively thicker crust (~ 10 to 15 km thick) with numerous magmatic additions. The distal NE SCS margin formed during the Cenozoic rifting of the SCS. The crust of the SH likely corresponds to a polygenic crust, recording polyphase magmatic activity since the Mesozoic, with potentially significant activity during Cenozoic post-rift time. The NE SCS margin is conjugate to Palawan, whose basement is interpreted to be part of the exotic Luconia microcontinent that collided with Eurasia during the Late Cretaceous. Basement similarities between Palawan and the SH are highlighted, suggesting that the latter might also be part of Luconia. Our results suggest that the suture between Eurasia and Luconia might have acted as a preferred zone for the Cenozoic rift development.