Sedimentological, paleontological, and geochemical data from core XK-1 on the Xisha Islands have allowed for a detailed documentation of the early carbonate development around the Oligocene-Miocene transition in the northern South China Sea (SCS). The deposits within the fore reef, reef, lagoon environments occurred before 23 Ma, the exposure horizon occurred around 23 Ma, and the sediments within the open lagoon setting dominated after 23 Ma. This evolution indicates a sedimentological response to water depth change, which is the combined result of eustatic sea-level fluctuations and tectonic subsidence. The tectonic subsidence during the latest Oligocene and Early Miocene (especially this period) was responsible for the obvious deepening trend. What's more, substantial physical erosion caused an increased amount of terrigenous input into the Xisha Islands area, with detrimental effects on carbonate development after the Oligocene-Miocene boundary. Over the entire South China Sea, the early carbonate systems along the northern and southern margins displayed specific evolution patterns. After comparing these patterns, we found a close relationship between the carbonate initiation and the subduction of the proto-SCS and the opening of the modern SCS. Therefore, it has been demonstrated that sea level and local tectonics as well as paleoclimatic conditions were the main controlling factors in shaping the onset of carbonate sedimentation in the SCS.