Planktonic foraminifera (PF) from Ocean Drilling Program (ODP) Sites 1143 and 1146 in the southern and northern South China Sea (SCS), respectively, were quantitatively analyzed in order to reconstruct the sea-surface environment over the last 12 Myr. The observed decrease in deep-dwelling PF species after ~10 Ma at both sites is interpreted to reflect a depression of the upper water thermocline, corresponding to the closure of the Indonesian Seaway around 11--9 Ma. This upper water column structure implies the intensification of equatorial Pacific warm currents and the initial formation of the western Pacific warm pool (WPWP) during the early Late Miocene. The consistent pattern of south-north thermocline evolution and the synchronous disappearance of Globoquadrina dehiscens (9.8 Ma) at both Sites 1143 and 1146 together imply that the entire SCS was likely under the influence of the newly developed WPWP at ~10 Ma. After ~8 Ma, sea-surface temperatures and thermocline variations evolved differently between the southern and northern SCS. The total deep-dwelling PF fauna at Site 1143 decreased gradually in abundance from 6.6 to 2 Ma, indicating a deepening of the thermocline in the southern SCS. In contrast, deep-dwelling PF species increased in abundance from 3.1 to 2 Ma at Site 1146, reflecting a shoaling of the thermocline in the northern SCS. This south-north contrast reflects two major environmental regimes: (1) the southern SCS, which has mainly been under the influence of the WPWP since the late Late Miocene, and (2) the northern SCS, where effects of the east Asian winter monsoon have prevailed, especially since the Late Pliocene. Estimate of past sea-surface temperatures (SSTs) at Site 1143 suggests a relatively stable and warm environment in the southern SCS since about 2.5 Ma, with an increased influence of warm subsurface waters after the mid-Pleistocene transition (1.2--0.9 Ma). In the northern SCS, however, a gradual decrease in winter SST recorded at Site 1146 over the last 4 Myr records east Asian monsoon evolution, especially the enhancement of the east Asian winter monsoon between 3.1 and 2 Ma.