Abstract: Joint inversion of the 1093 km of integrated geophysical detecting section (CFT) is made across the southwestern sub-basin of the South China Sea and the two sides of the continental margin. The data involved in the inversion includes the ocean bottom seismograph (OBS) data, the long-arranged multi-channel seismic profiles, and the gravity and magnetic profiles. Based on the results of joint inversion and segmented interpretation, many pre-Cenozoic residual sedimentary deposits and multiple periods of magmatic activities are observed. The crustal structure of the South China Sea is quite complex, which includes continental crust, thinned continental crust, continental-oceanic transitional crust and ocean crust. The high-speed layer under the crust is widely distributed. The observations prove that the joint inversion of gravity, magnetism, and seismic data is an effective tool to study the structural characteristics of the sea and deep crustal structures.