Abstract: Based on the comprehensive environmental investigations of the Yangtze River Estuary and its adjacent waters in May and November 2014, the migration, distribution, and mutual transformation of particulate organic carbon (POC) and dissolved organic carbon (DOC) were analyzed. The results showed that the DOC and POC concentrations of the Yangtze River Estuary as a whole follow the distribution pattern of high in the south, low in the north, high inshore areas, and low offshore areas. In spring, the DOC contribution rate of the Yangtze River Estuary ranged from 18.44% to 71.50% with an average of (46.78±13.87)%; in autumn, it varied from 25.46% to 84.97% with an average of (63.35±14.63)%. POC dominated inshore areas, especially near the turbidity maximum zone (TMZ), while DOC dominated offshores. Also, the DOC in the surface water is more advantageous than the bottom water. The organic carbon sources in the Yangtze River Estuary were complex, mainly contributed by terrestrial input sources, while the marine source and the delta source were higher at the bottom. There is a conversion of form ratio between DOC and POC in the Yangtze River Estuary, which is mainly controlled by the dynamical changes of salinity and total suspended matter (TSM) concentrations. When the TSM concentration was greater than 98.41 mg/L, the organic carbon in the Yangtze River Estuary was mainly in particulate, otherwise, it was mainly dissolved. Besides, TMZ played an important role in the transformation of organic carbon concentration and morphology, where POC began deposited and mineralized, as well as desorption caused by strong hydrodynamic forces and microbial degradation may promote its conversion to DOC.