The east Asian monsoon climate has an overwhelming influence on local climatic conditions of the South China Sea (SCS). Here we present results from a 3-year study of modern sediment traps from the central SCS in which the percentage of opal, the fluxes of Pulleniatina obliquiloculata and Globigerinoides ruber, the organic carbon flux, and primary productivity all show highest values during winter when the mixed layer depth is deepest. The δ18O difference (Δδ18O(P-G)) between the subsurface dwelling P. obliquiloculata and the mixed layer dwelling G. ruber in core top samples from 12 piston cores and one Ocean Drilling Program (ODP) site in the SCS is large, ~0.6? in a cold eddy area with a shallow mixed layer off Vietnam, but is reduced in deep mixed layer settings lacking cold eddies. We also present 1.56 Myr-long isotope records of G. ruber and P. obliquiloculata from ODP site 1143 in the southern SCS that reveal upper ocean thermal gradient variations during the Quaternary. Lower Δδ18O(P-G) values indicate increased mixed layer depths over most glacial episodes, likely due to stronger winter monsoon winds. In contrast, higher Δδ18O(P-G) values during interglacial intervals suggest decreased mixed layer depths and thus weaker winter monsoon winds. Comparisons of Δδ18O(P-G) with the percentage of P. obliquiloculata at site 1143 and the percentage of herbs and opal flux at site 1144 demonstrate that glacial-interglacial variations were strongly influenced by stronger and weaker east Asian winter monsoons during glacials and interglacials, respectively. Therefore the upper ocean thermal gradient variations in the SCS have been consistently affected by the east Asian winter monsoon since at least the beginning of the Pleistocene.