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The link between tropical cyclone (TC) activity in the South China Sea (SCS) and global climate change is commonly debated and there is a clear need for long-term geological records of TC activity if we are to clarify this connection. Multi-millennial, high-resolution paleo-storm records from the SCS are rare in the region and this causes difficulties for those exploring potential climate drivers of TC variability over centennial to millennial timescales and reduces our ability to fully assess the risks associated with future TC activity. This paper presents an age-constrained, mud-dominated sedimentary sequence from a coastal lagoon on Hainan Island, China. Multiproxy analyses incorporating chronological, lithological, sedimentological, and geochemical evidence were used to infer storm deposits preserved within the sequence and to reconstruct a time series of storm activity in the SCS during the mid-to-late Holocene. This long sedimentary record shows that TCs were highly active over the periods 5500 to 3500 and 1700 to 0 cal yrs. BP, and these periods contrast with a relatively quiet period 3500-1700 cal yrs. BP. An apparent inverse correlation between TC reconstructions from the SCS and those from the Korean Peninsula and Japan implies an oscillating pattern across the SCS and western North Pacific (WNP) over centennial to millennial timescales. A comparison between the sedimentary and paleoclimatic records implies that the El Nino-Southern Oscillation was not the only mechanism responsible for typhoon variability over the past 7500 cal yrs. BP, suggesting that other factors such as the thermal state of the western Pacific warm pool likely also had a strong influence on both SCS and WNP TC variability.