This paper is the result of hydrogeological survey engineering. Objective There are numerous water-intakes along the mainstream of the Yangtze River downstream, in order to ensure water safety and eco-environmental health, relevant situation of heavy metals in the nearshore sediment need to be studied urgently. Methods A total of 85 sediment samples were collected on both left and right banks from the upstream to the downstream with the investigation. Descriptive statistics analysis was used to show the characteristics of heavy metals. Correlational analysis and principal component analysis (PCA) were applied to study the sources of heavy metals. Geoaccumulation index and pollution load index were used to analyze the pollution levels, and the potential ecological risk of heavy metals were evaluated by the methods of potential ecological risk assessment index. Results The order of average content from high to low is Zn＞Cr＞Cu＞Ni＞Pb＞As＞Cd. From the upstream to the downstream, Cu、Zn、Cr、Ni had a small fluctuating but increasing trend, while As and Pb had a small fluctuating but decreasing trend, Cd showed decreasing trend with an obvious fluctuation. The most polluted one is Cd among seven heavy metals, which were mainly from human activities, such as agriculture. Cd accounted for 1.18%, 1.18%, 18.82% and 34.12% from polluted Class 1 to 4, respectively. Cr and Ni were non-pollution class, which mainly from industries and geochemical natural source. 34.18% of all sampling sites were in moderate pollution (1≤PLI_point＜2). RI was ranged from 19.48 to 388.62, and the proportions of slight potential ecological risk, medium potential ecological risk, strong potential ecological risk and extremely strong potential ecological risk were 38.82 %, 42.35 %, 17.65 % and 1.18 %, respectively. Conclusions Contents of all heavy metals in mainstream sediment of the Yangtze River downstream were at a lower level. The catchment were overall at non-pollution sate (PLI _area＜1)with slight to moderate ecological risk. The average contents, pollution levels and potential ecological risks of heavy metals on the right bank were all higher than those on the left bank.