The South China Sea (SCS) is an important moisture and heat source in the Asian monsoon system, and its environmental changes influence economic and social stability in Southeast Asia and East Asian. Previous records on sea surface temperature (SST) and salinity (SSS) were mostly from one sediment core, and/or only showed fragmentary information. It is hard to provide insights into the mechanisms of the overall paleoceanographical environmental variability in the northern SCS. In this study, paired δ18O and Mg/Ca records of planktonic foraminifer Globigerinoides ruber from Core S0204B nearby the Luzon Strait (21°13.818′N, 118°3.077′, water depth 1822 m), and Core GHE 27L (19.85°N, 115.34°E, water depth of 1533 m) in the central northern SCS, were analyzed, so as to better understand the physical process of the SST and SSS changes in the northern SCS and its relationship with the tropical Pacific. The results demonstrate that the SST is relatively stable and seawater δ18O (δ18Osw) values, a salinity proxy, shows a decrease trend since 7.0 ka BP in Core S0204B. By contrast, SST and δ18Osw in Core GHE 27L exhibit an overall increasing trend at the same time, indicating apparent regional discrepancy on the changing trend of the SST and SSS in the northern SCS. We suggest that the thermal and hydrographic conditions in Core S0204B were primarily influenced by the outer western Pacific water. However, the thermal and hydrographic conditions in Core GHE 27L may be predominantly controlled by the weakened Asian monsoon during the mid-late Holocene, which was induced by the southern migration of Intertropical Convergence Zone (ITCZ) and stronger EI Niño Southern Oscillation.