Between May 2004 and March 2005, samples of suspended particulate matter (SPM) were collected from the top 200m on five cruises to the South-East Asia time-series study (SEATS) Station. Isotopic and elemental analyses of the organic matter in these samples gave δ13C values ranging from −25.2‰ to −21.3‰ with a decreasing trend downward, and C/N ratios ranging from 5.5 to 11.4 with a weighted mean value of 6.74, which is very close to the Redfield ratio, suggesting a predominantly marine origin. The temporal isotopic variation in the surface layer has been successfully simulated with the algorithm based on diffusion-controlled carbon uptake during photosynthesis. The calculation of the carbon isotopic composition of phytoplankton was based on observed values of hydrographic, isotopic and chemical variables. It is noted that variations in the biological parameters, including the specific growth rate, enzymatic isotope fractionation during carbon fixation, cell size, and cell wall permeability, within the normal ranges may have contributed significantly to the observed isotope variability. According to simulation using the same algorithm, isotopically very light particulate organic carbon (POC) could be produced in the subsurface euphotic zone due to the much reduced specific growth rate, but the contribution of the subsurface production to the sinking flux was probably not significant. Sediment traps deployed from September 2001 to May 2002 in the northern South China Sea (SCS) provided samples for isotopic and elemental analyses of the organic matter. The measurements gave δ13C values ranging from −25‰ to −20.8‰ and C/N ratios ranging from 5.5 to 18. The isotopic variation of organic carbon in the sediment trap samples was successfully explained by the mixing of terrigenous organics (δ13C=−25.5‰ and C/N=22) and marine organics (δ13C=−22.1±1.1‰ and C/N=6.63±1). The latter composition is very close to the weighted mean composition of the suspended particulate organic matter (POM) from the top 20m, implying the surface water as the major source of organic matter in sinking particles. Compared to previously reported results of samples collected from the seafloor in the SCS, the inferred δ13C values of the marine organics in the sinking flux are lower than those (δ13C=−22.9‰ to −20.1‰) of the POC in the nepheloid layer, which are in turn lower than those of the organics (δ13C=−21.5‰ to −18.8‰) in surficial sediments. The progressively heavier POC below the top 200m is contrary to the trend of decreasing δ13CPOC in the top 200m. We have demonstrated that the Suess effect and the elevated concentration of aqueous CO2 in the surface water due to the increasing atmospheric CO2 partial pressure may cause depletion of 13C more than enough to account for the observed depression of δ13C values in the progressively younger POM. In the past, diagentic isotopic alteration has been proposed as the process responsible for both the decreasing trend of δ13CPOC in the surface layer and the increasing trend in the subsurface layer. Although the diagenetic effect cannot be ruled out, this study shows that other processes are sufficient to explain the observed trends of isotopic variation of POC.