High-resolution records of past environments of the South China Sea (SCS) could provide important information to better understand the mechanisms of El Niño Southern Oscillation (ENSO) and East Asian monsoon evolution since SCS is located between Pacific Ocean and Eurasian continent. SCS plays a key role as the moisture source area of monsoon precipitation that affects the terrestrial climate of Asia. Fossil and modern corals were obtained from South China Sea (SCS) to study changes in oceanographic conditions when the northern hemisphere experienced perihelion during the early to mid-Holocene and thermal contrast between SCS and the Asian continent was larger. The fossil coral is 6600 years old and XRD and SEM investigations confirmed pristine nature of this sample. Oxygen isotope measurement of modern coral yielded an average value of ca. −6‰, whereas the fossil coral showed ca. −5.5‰. Given that previously reported alkenone SST thermometry and foraminiferal SST reconstruction indicate little changes in SST (<0.5°C) throughout the Holocene in SCS, we consider the possibility of changes in δ18O of seawater to be due to local sea surface salinity (SSS). Coral data from the present study (6600 years old coral) as well as previously published record (4400 years old) showed higher SSS during the mid-Holocene. Coral data were then compared with the coupled Ocean-Atmosphere GCM (MIROC3.2). Higher SSS during the mid-Holocene time was also seen in AOGCM experiments. We observed northward shift of inter tropical convergent zone (ITCZ) in the experiments that produced increased precipitation on the Asian continent. The cause of increase in salinity was, therefore, due to less precipitation in SCS and increased continental precipitation inland of Asia.