The investigations on the organic carbon (OC) of core sediments were carried out in Chongming east tidal flat (CM) during Scirpus mariqueter growing stage (from April to December 2004) in Yangtze Estuary. The Yangtze River annually transports a runoff discharge of 30,000 m3/s,carrying about 480 million tons of sediments to the estuarine and coastal area, which formed a great OC pool. In the sampling spots, seven quadrats of 50 cm × 50 cm and five sediments cores of 20 cm deep (40 em deep in December) were randomly established in order to collect vegetations and core sediments samples during the low tide each month except November. After pretreatment, the core sediments were sieved and their OC contents were measured according to the potassium dichromate method. The results show that the higher surface sediment OC content in summer comes from allochthonous terrigenous particle settlements on the Chongrning east middle tidal flat S. mariqueter zone. In autumn and winter, the decomposing of the defoliated S. mariqueter increases the surface sediments OC content. Settling velocity, sediment temperature and S. mariqueter growth are the main factors that can control the sediment carbon content. Summer is the "carbon losing" period of the tidal flat sediments, while from September, it changes into the "carbon accumulating" period of sediment OC pool because of the decomposing of dead S. mariqueter community in the sediments. From this altemation of "carbon losing" period and "carbon accumulating" period, we conclude that carbon in the OC pool of the middle tidal flat S. mariqueter zone sediments mainly comes from the atmospheric carbon rooted by S. mariqueter photosynthesis.