Time-series sediment trap materials at different water depths and surface sediments in northern and central South China Sea (SCS) were analyzed for organic carbon, amino acids, amino sugars and carbohydrates. Results show that particulate organic carbon (POC) is mainly derived from marine plankton, only 1.4%—1.6% of primary production sinks into deep SCS water column and less than 0.22% of primary production ultimately reaches the sediments. The remineralization and dissolution of organic matter as well as the compositional alterations of organic matter mixtures may mainly take place in the upper few hundred meters of water column, deep carbonate (opal) lysocline zones, and interface layers between sediments and water column, rather than in mid-waters. The organic geochemical parameters such as (T_(AA)+T_(SUG))OC%, AA/AS, Gluam/Galam, Arom. AA/non-prot. AA, ASP/b-ALA, Glu/gABA decrease from living marine plankton (or planktonic shells), to settling particulate matter and to sediments suggesting that th Time-series sediment trap materials at different water depths and surface sediments in northern and central South China Sea (SCS) were analyzed for organic carbon, amino acids, amino sugars and carbohydrates. Results show that particulate organic carbon (POC) is mainly derived from marine plankton, only 1.4% -1.6% of primary production sinks into deep SCS water column and less than 0.22% of primary production ultimately reaches sediments. The remineralization and dissolution of organic matter as well as the compositional alterations of organic matter mixtures may mainly take place in the upper few hundred meters of water column, deep carbonate (opal) lysocline zones, and interface layers between sediments and water columns, rather than in mid-waters. The organic geochemical parameters such as (T_ (AA) + T_ AA / non-prot. AA, ASP / b-ALA, Glu / gABA decrease from living marine plankton (or planktonic shells), to settling particulate matter and to sediments Suggest that th