Based on a fully-coupled, high-resolution regional climate model, this study analyzed three-dimensional temperature and momentum changes in the South China Sea (SCS) from 1970 to 2000, during which period the climate shifts from a decadal La Niña-like condition (before 1976/77) to a decadal El Niño-like condition afterward. With a set of partially-coupled experiments, sea surface temperature (SST) and kinetic energy (KE) changes during this period are first decomposed into two components: those induced by lateral boundary forcing and those induced by atmospheric surface fluxes. The results showed that the total SST and KE changes show an increasing trend from 1970 to 2000. The two decomposed components together determined 96% and 89% of the SST and KE changes respectively, implying their dominant roles on the SCS’s surface variability. Spatially, a sandwich pattern of air-sea forcing relationship is revealed in the SCS basin.