Abstract: To reconstruct the provenance evolution since the Middle Miocene and identify its controlling factors on sedimentation pattern in the South China Sea, the mechanisms of differential sedimentation between the eastern and southwestern sub-basins of the South China Sea were studied. Core samples from IODP Expedition 349 Sites U1431, U1433, and U1434 were used, and geochemistry of element and Sr-Nd isotope were analyzed systematically. Results reveal distinct sedimentary histories. Chemical weathering indices (CIA) indicate that the southwestern sub-basin (Site U1433) experienced persistently stronger chemical weathering than the eastern sub-basin (Site U1431) since approximately 6 Ma, highlighting a fundamental difference in source-area weathering regimes. Rare earth element signatures and La-Th-Sc systems show that sediments in the two sub-basins are derived mainly from felsic upper continental crust. However, the eastern sub-basin records a significant influx of mafic volcanic or seamount-derived materials during the Middle-Late Miocene. A major provenance reorganization occurred in ~8 Ma as indicated by Sr-Nd isotopes. Following this shift, the eastern sub-basin had been dominated by northern terrigenous sources (Pearl River and Taiwan Island), whereas the southwestern sub-basin remained under the sustained influence of western sources, mostly from the Indochina Peninsula (e.g., the Mekong River). This pivotal transition entailed a provenance change from volcanic-domination to northern terrigenous-domination in the eastern sub-basin. In contrast, the southwestern sub-basin’s provenance was more sensitive to local tectonic-fluvial events (e.g., uplift of the East Vietnam Marginal Plateau, migration of the Mekong River estuary). The observed sedimentary differentiation since the Middle Miocene fundamentally stems from differential responses of the two sub-basins to a common series of regional tectonic events. This differentiation pattern was governed by provenance shifts driven by these tectonic movements, which was further modulated by the basin topography and ocean current systems.