Abstract: The South China Sea (SCS), under the control of multiple climate patterns, is an ideal region for studies of paleo-climate and the East Asian monsoon. In this paper, we studied the composition and characteristics of isoGDGTs to further identify their sources and used the outspread TEX^H₈₆ index to reconstruct the sea surface temperature (SST) of the northern SCS for the past 31 ka quantificationally. By calculating the Methane Index and BIT indexes, we found that the isoGDGTs mainly came from Thaumarchaeota, and are suitable for TEX^H₈₆ appliance. TEX^H₈₆ temperatures exhibit distinct glacial–interglacial cycles, and is very similar to the SSTs from foraminifera and U^K'₃₇ in the northern SCS. TEX^H₈₆ SSTs showed a decline trend during the Heinrich events (H1-3) and an abrupt rise at 14.6 kaBP before Bølling–Allerød (BA) warming, suggesting a tight climate teleconnection between the northern SCS and the North Atlantic region in last Deglaciation. The SST differences (ΔSSTs) between the SCS and the core MD01-2421 in the North Pacific was calculated and used to reveal the intensity of East Asian Winter monsoon. ΔSSTs showed that the EAWM intensity firstly increased before the BA warming, reached a maximum in the Younger Dryas period, decreased again in early Holocene and slowly increased in Late and Middle Holocene. The ∆SSTs results coincide with previous findings on the EAWM variations and constitute a feasible means of long-term EAWM intensity reconstruction.