A three-dimensional (3D) P-wave seismic velocity (Vp) model of the crust at the northern South China Sea margin drilled by IODP Expeditions 367/368/368X has been obtained with first-arrival travel-time tomography using wide-angle seismic data from a network of 49 OBSs and 11 air-gun shot lines. The 3D Vp distribution constrains the extent, structure and nature of the continental, continent to ocean transition (COT), and oceanic domains. Continental crust laterally ranges in thickness from ~8 to 20 km, a ~20 km-width COT contains no evidence of exhumed mantle, and crust with clear oceanic seismic structure ranges in thickness from ~4.5 to 9 km. A high-velocity (7.0-7.5 km/s) lower crust (HVLC) ranges in thickness from ~1 to 9 km across the continental and COT domains, which is interpreted as a proxy of syn-rift and syn-breakup magma associated to underplating and/or intrusions. Continental crust thinning style is abrupter in the NE segment and gradual in the SW segment. Abrupter continental thinning exhibits thicker HVLC at stretching factor (β) <~3, whereas gentler thinning associates to thinner HVLC at β>~4. Opening of the NE segment thus occurred by comparatively increased magmatism, whereas tectonic extension was more important in the SW segment. The Vp distribution shows the changes in deformation and magmatism are abrupt along the strike of the margin, with the segments possibly bounded by a transfer fault system. No conventional model explains the structure and segmentation of tectonic and magmatic processes. Local inherited lithospheric heterogeneities during rifting may have modulated the contrasting opening styles.