Abstract: The South China Sea is one of the largest marginal seas in the Western Pacific. It is located at the transition and junction of the Eurasian Plate, the Philippine Sea Plate and the Indo-Australian Plate and contains a wealth of cutting-edge geoscience issues.Based on the previous ocean drilling expeditions (ODP184, IODP349, IODP367, IODP368, and IODP368X) in the South China Sea, the important progresses were summarized systematically since the Mesozoic, including the basin rifting, seafloor spreading, climate change, and sedimentary evolution respectively. Focusing on the Spatiotemporal heterogeneity during the evolutionary process of the conjugate continental margin, four scientific themes are proposed, such as the extension and thinning process of the continental margin, the rift process of the ocean-continent transition zone, the dynamic mechanism of magmatic activity. Most of the previous oceanic drilling expeditions are constrained to the middle part of the northern continental margin of the South China Sea, and have limited control on the entire South China Sea. In order to solve the above scientific problems, 9 drilling sites are proposed in the northeast sub-basin, southwest sub-basin and northwest sub-basin of the South China Sea through the detailed interpretation of the relevant data. Thus, a comprehensive, complete and specific evolution process of the South China Sea will be revealled. Adhering to the principle of combining the depth and the shallow, and the combination of difficulty and ease, the proposed sites will be carried out for the implementation of the South China Sea ocean drilling in the future, which not only has the practical needs to support the future drilling and mining of natural gas hydrate in the South China Sea, but also has important scientific significance for depicting the complete life history of the South China Sea.