Abstract: In order to explore the characteristics of occurrence and status of pollution of heavy metals in surface sediments in the southeastern branch of the Yangtze River estuary, 18 surface sediment samples were collected in Yangtze River estuary in December 2019. The total content and the levels of each morphology of the seven sediment heavy metals (Cu, Pb, Cd, Cr, Zn, As, Ni) were analyzed based on methods of microwave digestion and the improved continuous extraction. Moreover, the ecological risks of heavy metals were evaluated by deposition methods such as sediment quality guideline (SQG) and hazard quotients (HQ). The results showed that the concentrations of heavy metals gradually decreased from nearshore to offshore. Most of heavy metals all reached China's marine sediment quality Class I standard, except for Cd and Cr (Class II standard). The sediments in the researched area were neutral-weakly alkaline and presented a reducing environment. Zn, Pb, and Cd mainly presented in secondary facies, which are more sensitive to the environmental conditions. Among them, the Cd secondary facies had the highest ratio (74.2%), and the reducible state was the main occurrence form. In addition, the stable primary phase of Cu, Cr, As, Ni was the main occurrence form. Ecological risk assessment results showed that it was found that the combined biological effects of heavy metals in the surface sediments of the Yangtze River estuary had low probability of affecting aquatic organisms. As and Cd had a higher risk of ecological hazards than other metals, especially Cd as it was easy bio-utilization and threatened to the environment, therefore, we should pay attention to the element Cd.