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As a natural laboratory for testing various paleoclimatological and paleoceanographic hypotheses, the Pliocene-Pleistocene stratigraphic sequence from a full-coring major scientific drilling (Well CK2 with total length: 928.75 m) in Yongle atoll of Xisha Islands, northern South China Sea was studied. The Petrography of studied section of the core was dominated by reef carbonate limestones which contain abundant shallow marine organisms, e.g., coralline algae, corals, and foraminifera, which almost consisted of pure carbonates and preserved the primary geochemical message since Pliocene. According to the isolation of Well CK2 and the provenance of elements, the systematic changes and abrupt points of isotope and element geochemical compositions (rare earth element parameters, SiO2 content, Al/Ti ratio, etc.) from coral reef carbonate record presented the elevated terrigenous influences related to the East Asian monsoon after similar to 2.6 Ma BP, as part of the Pliocene-Pleistocene climate transition. Our results demonstrated that the continental weathering controlled by the East Asian summer monsoon dominated the surface seawater compositions of study area before similar to 2.6 Ma BP, when the winter monsoon was not strong enough to exert significant influences. Then, the effects of eolian dust associated with the intensity of East Asian winter monsoon, the precipitation driven by summer monsoon, and the global temperature, which played different roles at different periods after similar to 2.6 Ma BP, should be considered. Our results confirmed that the potentials and significances of shallow-water carbonate deposition from coral reefs, and provided a unique perspective to shed light on the carbonate record of climate changes.