Evolution of the continental margins of the South China Sea (SCS) is one of the open questions when discussing continental breakup and seafloor spreading. We processed data from a wide-angle seismic profile (OBS2011–1), which passes through the northwestern margin of the SCS, and performed travel time modeling to obtain the seismic velocity structures. The modeling results show a stepwise variation of the crustal thicknesses from continental margin to oceanic basin. Stretching factor of the upper crust is nearly double the estimate of the lower crust along the Zhongsha Trough. The lower crust shows asymmetrical upwelling towards the trough center, accompanied by ∼0.3 km/s of the velocity increase due to magmatic addition. The upper and lower crusts have almost the same stretching factor beneath continental blocks, indicating a uniform extension. Crustal structures of the conjugate margins of the Southwest Sub-basin show similar velocity range and different thickness distribution, supporting the common origin and asymmetric extension of these two margins. The Ocean-Continent Transition zones (OCT) are much wider in the southern part (∼50 km) than the northern part (∼25 km) crossing the margins. We propose a tectonic model for the asymmetry of both the conjugate margins and the OCTs, favoring the highly stretched upper crust and accompanied by rising of the ductile middle-lower crust controlled by major low-angle faults. The rigid blocks may also act as a kind of hindrance for further evolution of the failed rifts and affect the shape of the OCT.