This paper presents a comprehensive study of crustal structure by using gravity inversion for interface with seismic data constraints to invert depth of the Moho and to calculate crustal thickness, and by performing gravity anomalies correlative imaging method without constraints to construct the 3D subsurface distribution of equivalent density in the South China Sea. The integrated geophysical analysis along the Guangzhou-Palawan geosciences transect demonstrates that the characteristics of the gravity anomalies and their inversion results allow us to reveal crustal structure and regional tectonics features in the large scale of the South China Sea.