The continental margins of the South China Sea (SCS) have undergone episodic rifting since the Cenozoic, and there are ongoing debates surrounding the processes of crustal deformation and seafloor opening. In this work, we present a P‐wave velocity model extending from the north of Xisha Trough to the Zhongshanan Basin in the northwestern SCS margin, using ocean bottom seismometer data of the wide‐angle seismic profile OBS2013‐1. The results show that the crust thins symmetrically across the western Xisha Trough, from more than ∼20 km at the flanks to ∼10 km in the central valley where the sedimentary layers thicken to over 6 km. In the Zhongsha Trough, closer to the deep basin, the upper crust is detached in a ∼20 km wide region and the lower crust has seismic velocities increased by more than ∼0.3 km/s. The top boundary of the lower crust is located at a depth of ∼13 km across the Zhongsha Trough, and a ∼5 km thick midcrustal ductile layer is imaged. A ∼50 km wide ocean‐continent transition region beneath the Zhongshanan Basin characterizes a ∼6 km thick continental crust underlain by serpentinized and magnetized upper mantle. These observations, together with plate reconstructions based on gravity and magnetic analysis, suggest that deformation of the continental margin was controlled by a ductile crustal layer. Magmatism, associated with the early stage oceanic accretion, has mixed with the highly extended continental crust. Developments of the failed rifted basins were controlled by the westward propagation of the continental breakup.