Organic carbon isotope ratios, abundance of alkenones and particle size data reveal hydrological changes during the Holocene in the northern South China Sea. There is no strong anti-phase or co-variation between winter and summer monsoon throughout the Holocene. The alkenone-based SST reconstruction shows rapid warming in the first 1500 years of the Holocene and relatively stable SST in the past 9000 years. There is a clear difference between coastal SST history and oceanic SST history in the northern South China Sea. Several short-term ‘Bond Events’ are recorded in this low latitude location.