Calcareous nannofossils deposited in deep-sea sediments are a good proxy of surface water paleoproductivity. Quantitative micropaleontological and stable isotope analyses were performed on Quaternary calcareous nannofossils from ODP Site 1143 in the southern South China Sea. Changes in absolute abundance, accumulation rate and carbon isotope record of nannofossils were used to understand the Quaternary evolution of surface water paleoproductivity in the southern South China Sea. The results show that surface water paleoproductivity displayed significant oscillations on two different time scales during the past 1.56 Ma. One is the fluctuation in paleoproductivity that covaried with glacial-interglacial cycles during glacial periods. The other fluctuation in paleoproductivity involved long-term changes on a time scale of about 400 ka.