The sediments distributed in the marginal seas of the continental shelf are important burial materials for global organic carbon (OC). There have been many estimates of the global continental shelf OC reserves, but due to the limited acquisition of measured data, the estimated results have great uncertainty. The vast continental shelf in the northern part of the South China Sea (SCS) provides a good place for the storage of OC. Based on a large amount of sediment OC data obtained from the northern coast of the SCS, the OC storage in the surface sediment (0~10 cm) in the study area (approximately 8.63 × 104 km2) was accurately calculated as 51 Tg. The study area covers different regions, such as estuaries, open seas, strait areas and upwelling development areas, and the OC content of each area is quite different. According to provenance analysis, the source of OC in sediments is mainly from the input of Pearl River runoff. The OC content is significantly higher and less affected by sediment particle size in the Pearl River Estuary and the surrounding areas; meanwhile, the OC content gradually decreases with the distance from the Pearl River Estuary. Far from the western Pearl River Estuary, the sediment OC content is mainly controlled by the particle size of the sediments and is significantly correlated with silt and clay content. The deposition rate is also an important factor affecting the burial of OC, for the high deposition rates correspond to the high levels of OC in the nearshore estuarine areas, as well as the low deposition rate region having low OC content in the sediments even though it has a high productivity of OC, such in as the upwelling sea area on the eastern side of Hainan.