<p>The South China continental margin spans various land-sea tectonic units, including the Jiangnan orogenic belt, the Cathaysia Block, and the northern margin of the South China Sea, exhibiting significant crustal structural differences. The widespread exposure of Mesozoic granites in South China reveals extensive tectonic-magmatic activities in the region. Therefore, in-depth research into the deep structure of the South China continental margin is of great significance for understanding the tectonic evolution and resource effects of the area. This paper focuses on the South China and northern South China Sea regions, employing the Hamiltonian Monte Carlo (HMC) three-dimensional density gravity inversion method, combined with deep seismic sounding and ocean bottom seismometer data, to establish a three-dimensional density model covering the land-sea extent of the South China continental margin. The density structure reveals Moho depths of 28–48 km in the South China continent, 22–28 km in the northern margin of the South China Sea, and 10–20 km in the northwestern sub-basin, with the Moho surface rising from land to sea. Based on the density characteristics of granites in the region, the possible distribution ranges of granite bodies are delineated. The results show that the bottom boundaries of the Miaoershan-Yuechengling and Zhuguangshan-Wanyangshan granite bodies extend approximately 12–15 km, while the bottom boundaries of the Fogang and Darongshan-Shiwandashan granite bodies are at depths of about 4–5 km. The crustal structure of the South China continental margin thickens from sea to land, superimposed with local crustal thinning, reflecting the complex tectonic changes of the South China continent and the comprehensive influence of multi-phase tectonic-magmatic activities. The depth distribution of large granite bodies inferred from the density structure provides a basis for exploring deep tectonic-magmatic activities and their impact on mineralization in the region.</p>