The South China Sea plays a key role to change the precipitation variability in East Asia by influencing the northward moisture transport. Previous study found that there exist changes in atmosphere–ocean interactions over the South China Sea (SCS) before and after the late 1990s during boreal summer (June–July–August) in the observations. This study further supports such changes using two simulations of the atmospheric regional climate model (RCM) forced by historical sea surface temperature (SST). The control run is forced by historical SSTs, which are prescribed in the entire domain in the RCM. In addition to the control run, an additional idealized experiment is conducted, i.e., the historical SSTs are prescribed in the SCS only and the climatological SST is prescribed outside the SCS to examine the changes in the atmosphere–ocean interactions in the SCS. It is found that the simultaneous correlation coefficient between SST and precipitation changes significantly over the SCS before and after the late 1990s. This result supports the notion that there are significant changes in atmosphere–ocean interactions over the SCS before and after the late 1990, which affects the ability of the RCM to simulate precipitation variability accurately relative to observation. This result implies that the simulations of atmospheric circulation model results forced by observed SST before the late 1990 should be cautiously interpreted because the observed SST anomalies are forced by the atmosphere.