Marine sediment is an important sink of organic carbon in marine biogeochemical cycles. As a novel but powerful tool, compound-specific isotopic analysis of amino acids (CSIA-AA) was applied to trace the origin and fate of organic matter. Stable carbon isotopic values (d13C) of individual amino acids and bulk organic carbon were analyzed in surface sediments collected along the Pearl River Estuary in the winter of 2016. Primary result shows that the d13C values of sediment amino acids gradually increased along the studied salinity gradient, implying an origin of sediment amino acids from in situ production of phytoplankton. Our result indicaets that d13C values of amino acids is a good tracer to distinguish the origins of labile organic matter in sediments. Moreover, we found that sediment amino acids are more enriched in d13C than those of bulk sediment organic carbon, but both of them have similar pattern of distribution along the salinity transect. This indicates that organic carbon in the water column may experience a non-selective deposition during the early diagenetic process.