Down-core variations in planktonic foraminifera (PF) at Site 1143 (ODP Leg 184) disclose the evolution of the structure of the upper water column in the southern South China Sea over the last 12 Ma. In the early Late Miocene (-10.6-7.8 Ma), there existed a lower percentage of total deep-dwelling species, reflecting a water thermocline that was deeper than that in the Middle Miocene, which resulted from the closure of the Indonesian Seaway and relevant intensification of the equatorial warm current. After the increase in deep-dwelling PF and the rising of the thermocline during the late Late Miocene (7.6-6.4 Ma), the total deep-dwelling species decreased gradually from the late Late Miocene (6.4 Ma) to the Pliocene, implying the deepening of the water thermocline. The evolution of thermocline depth in the southern South China Sea reflected by the PF at Site 1143 might be a good indicator of changes in the West Pacific "warm pool".