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We present astronomically tuned high time resolution (3–4 kyr) benthic foraminiferal δ 18 O and δ 13 C records between 9 Ma and 5 Ma from Ocean Drilling Program (ODP) Site 1143 in the southern South China Sea (SCS). We found that the late Miocene ocean carbon shift (LMOCS) which was linked with the late Miocene/early Pliocene “Biogenic Bloom” also occurred in the northern and southern SCS. A marked deep-water δ 13 C gradient as much as ~ 1.0‰ of the northern and southern SCS was observed between 6.5 Ma and 5.9 Ma, which was probably caused by the significant difference in paleoproductivity between the northern and southern SCS. The deep δ 13 C gradient was likely produced by rapid tectonic subsidence in the northern SCS at ~ 6.0 Ma and the final formation of the Bashi Strait at ~ 6.5 Ma. A reversed benthic δ 13 C gradient of the northern and southern SCS was also observed between 1.2 Ma and 0.35 Ma, which was probably caused by the consecutive closures of the interarc water gates within the Bashi strait at ~ 3.0 Ma and ~ 1.2 Ma. Closures of the interarc water gates within the Bashi strait at ~ 3.0 Ma and ~ 1.2 Ma further semi-enclosed the SCS basin and made the paleoproductivity the major factor influencing the deep water δ 13 C, leading to the reversed deep water δ 13 C gradient of the northern and southern SCS between 1.2 Ma and 0.35 Ma. [ABSTRACT FROM AUTHOR]