The continent-ocean transition (COT) zone in the northern South China Sea (SCS) continental margin is a transitional zone from thinned continental crust to normal oceanic crust, which records important information about how the SCS progressing through rifting, breakup to seafloor spreading. The seismic profile OBS2018-H2 is parallel to a tectonic strike of the northern continental margin. It crosses through the drilling sites U1499 and U1502 of IODP (International Ocean Discovery Program). By using the combination of Raylnvr forward modeling and Tomo2d inversion software, we have obtained the seismic velocity structure as deep as the upper mantle along the OBS2018-H2 based on the travel-times data from 10 OBSs (ocean bottom seismometers) recording data. The velocity structure is divided into three parts : the western thinned continental crust region (0 similar to 63 km), the central COT region (63 similar to 120 km), the eastern exhumed middle- and lower-crust region (120 similar to 180 km) combined with high-resolution reflection data and IODP367/368/ 368X drilling data. The mechanism of rifting-breakup is discussed and built in the northern SCS continental margin combined with multi-channel reflective profile (Lw7). The continental crust of the northern SCS margin was stretched and thinned rapidly from late Eocene to early Oligocene (34 similar to 30 Ma), which triggered a rapid upwelling of the asthenosphere and the intrusion of magma into the crust. A large amount of molten material upwelled at similar to 30 Ma, invaded and destroyed the thinned continental crust, then triggered the rupture of the continental crust. The continental margin rapidly transitioned into igneous crust accretion (similar to 28. 7 Ma) and formed a relatively narrow COT. This research displayed the deep crustal structure of the COT area in the northern SCS continental margin and revealed the interactions between tectonics and magmatism, which further provided important references for the rifting-breakup process in global rifted margins.