The detailed lithospheric structure of South China is the basis for the understanding of tectonic processes of eastern China. Specifically, two essential issues in the study of lithospheric structure are the thermal and compositional structures, which are usually derived from either geophysical or geochemical observations. However, inversions from single geophysical or geochemical datasets have certain limitations, making it necessary to develop joint inversions of geophysical, geochemical and petrological datasets. In this paper, through thermodynamic simulation and probabilistic inversion, we inverted multiple datasets including topography, geoid height, surface heat flow and surface wave dispersion curves for the 3D lithospheric thermal and compositional structure of South China. The results reveal a thin (< 100 km) and flat LAB beneath the South China Fold System Block and the lower Yangtze Craton. Also, we found that the lithospheric mantle is primarily composed of saturated peridotite, indicating that the ancient refractory lithospheric mantle has been replaced by new materials. The dominant dynamic mechanism for lithospheric thinning in eastern South China may be the flat subduction of ancient Pacific slab, while thermal erosion may have also played a significant role. In contrast, the LAB depth beneath the Sichuan Basin is much thicker (> 200 km), suggesting that the thick and cold craton lithospheric roots are retained. There may exist a discontinuous interface beneath the Sichuan Basin, with the saturated lower layer thicker than the refractory upper layer. As a result, the lithospheric mantle of the Sichuan Basin and surrounding regions is mainly composed of saturated and transitional peridotite.