Studying the carbon dynamics of estuarine sediment is crucial to understanding of carbon cycle in the coastal ocean. This study is to evaluate the mechanisms regulating the dynamics of organic carbon in surface sediment of the Yellow River Estuary (YRE). Based on data of 15 surface sediment cores, we found that TOC (0.2-4.4 g kg-1) and TN (0.06-0.68 g kg-1) were generally higher to the north than to the south, primarily due to the differences in kinetic energy level (i.e., higher to the south). The C:N ratio ranged from 2.1-10.1, with highest value in the southern bay, and the lowest in the shallow water area near the river mouth. A considerable spatial variability in the δ13Corg values (-24.26‰ to -22.66‰) showed more negative near the river mouth and its adjacent south bay, and less negative far away from the river mouth and the coast line. Our analysis suggested that TOC was mainly from marine sources in the YER, except in the southern shallow bay where approximately 75% of TOC was terrigenous. Higher levels of TOC (with more negative δ13Ccarb) were not a result of local biological production. The current system would cause re-distribution of POC thus more TOC in the surface sediment. The overall low levels of TOC were due to profound resuspension that could cause enhanced decomposition. Further studies with integrative and quantitative approaches are needed not only to assess the spatial and temporal variations of major carbon forms in the water column and sediments, but also to quantify the contributions of various sources and transformations among the different carbon pools, which aims to better understand the carbon cycle in the YRE in the changing environment.