Mangroves have received increasing attention in recent years for their high carbon storage capacity. The effects of sea-level change during the last glacial period on terrestrial deposition and coastal mangrove ecosystems were investigated using various organic lipid proxies in marine sediment cores from the Sunda Shelf in the southern South China Sea (SCS). The gradual reduction in the content of long-chain n-alkanes and n-alkanols, BIT index, and increasing δ13Corg trend from the last glacial to the Holocene indicated that the depocenter moved landward from the studied location during the deglacial sea-level rise. Remarkable peaks in the mangrove proxy (Taraxerol/n-C28 alcohol ratio) occurred during meltwater pulse (MWP) events in the Sunda Shelf area, associated with the drowning and destruction of mangroves that could not withstand the rapid sea-level rise. The decomposition of carbon-rich mangrove deposits may have contributed to atmospheric CO2 concentration during two strong MWP events in Sunda Shelf. Our results suggest the vulnerability of mangrove systems upon rapid sea level change with positive feedback for global warming.