High-resolution carbonate stratigraphy and XRF core-scanning elemental geochemistry were analyzed at Core MD05-2899 in the upwelling area of the western South China Sea to reconstruct the evolution history of the East Asian Summer Monsoon (EASM) over the past 540 ka in the late Quaternary and to study the effect of sea level change on terrigenous material supply to the western South China Sea. Three proxies of elemental ratios were chosen for indicating paleoenvironmental changes: ln(Ba/Al) for the paleoproductivity, ln(Br/Al) for the organic matters, and ln(Ti/Al) for the terrigenous material supply. Our results show that the EASM has been continually enhanced over the past 540 ka and presents strong glacial-interglacial cyclicity with strengthened intensity during interglacials and vice versa. The EASM could be the major factor controlling the variation pattern of organic matters in the western South China Sea. The strengthened EASM could directly enhance the precipitation on lands surrounding the South China Sea, increase the runoff of their drainage basins, and finally produce higher terrigenous material supply during interglacial than glacial periods in the western South China Sea. However, when the relative sea level was lower than 60 m during glacial periods, the broad part of the Sunda Shelf was exposed and enormous amount of terrigenous materials could be eroded and then transported far to the western South China Sea, resulting in the strong terrigenous material supply during glacial maximum periods at Core MD05-2899. Therefore, we suggest that the late Quaternary EASM and sea level change could jointly control the variation of terrigenous material supply in the upwelling area in the western South China Sea.