We calculate the gravity anomalies due to lateral changes in bathymetry from an independent topography compilation, and those due to changes in sediment thickness and density. To obtain the Moho depth and the crustal thickness of the South China Sea basin, the 3‐D gravity inversion method is employed, based on an “initial model of fluctuating interface” constrained by the control points from seismic data and sonobuoys. And then, the gravity data is corrected for the lithospheric thermal gravity anomaly within continental margin due to lithosphere thinning. Over most of the South China Sea basin, the Moho depth ranges between 8∼14 km, the crustal thickness is 3∼9 km. The NNE trending fossil spreading center of the East and the Southwest Basin extend to 112°E, the Moho depth is more than 12 km, the crustal thickness is above 6 km in the spreading center. However, the crust of the spreading center at the northwest basin is not obviously thickened. In the northern margin of the southwest basin, south of Zhongsha block, there is a crustal thinning belt, nearly EW trending, where the crustal thickness is about 9∼10 km. The 14 km isoline of the Moho depth and the 9 km isoline of the crustal thickness are very close to the Continent‐Ocean Boundary.