Due to its unique geographical location and complex geological evolution processes, the South China Sea has been a focus of extensive research. Previous studies on the density structure of the South China Sea mostly focused on 2D density structures, with relatively limited research on 3D density structures. A comprehensive study is still needed to refine the expansion mechanism and tectonic evolution of the South China Sea. In this study, we utilized wavelet multi-scale analysis of gravity data to obtain a 3D density model of the South China Sea and discussed its tectonic evolution from the pattern of density anomalies. The inversion results show that (1) the expansion of the South China Sea caused the typical thin oceanic crust and parts of the continent–ocean transition zone may fracture due to the expansion; (2) the low-density anomaly in the upper mantle of Luzon Island may indicate partial melting or the upwelling of asthenosphere materials; and (3) the expansion of the South China Sea is influenced by multiple plate forces and uneven forces affect the distribution of high-density anomalies in the upper mantle.