In this study, content and distribution of organic matters (OM) and lipid biomarkers in surface sediments from northern South China Sea (SCS) were identified to reveal the sources and transport of fine-grained sediments. Organic matters and lipid biomarkers exhibited distinct spatial variation in northern SCS. Terrestrial discharge from the Pearl River and some mountainous rivers in southwestern Taiwan may contribute to the relatively high organic matters in the corresponding sea areas. The detection of unsaturated fatty acid homologues suggested the algal and/or bacterial OM contribution to surface sediments. The composites and distribution of lipid biomarkers indicate their mixed sources from terrestrial plants, marine algae and bacterial. Together with the proof of clay mineral composites in the sediments, the results suggested that the currents, including the Guangdong Coastal Current and Kuroshio Current, control the transport and distribution of terrestrial sediment and the sedimentary environment in the northern SCS.