In order to explore the ecological environment of the sea area near the Acipenser sinensis reserve in the Yangtze River Estuary, the seasonal variation and spatial distribution characteristics of heavy metal elements in surface seawater and sediments were analyzed. The comprehensive pollution index method and potential ecological risk index method were used to evaluate the heavy metal pollution degree and ecological risk grade. The results showed that the average concentrations of heavy metals Hg, As, Cu, Pb, Cd, Cr and Zn in seawater in 2018 was 3.852 μg/L, 1.948 μg/L, 6.362 μg/L, 4.542 μg/L, 0.294 μg/L, 6.201 μg/L, 44.56 μg/L, and Hg, Cu, Pb and Zn all exceeded national first-class seawater quality standards; the average concentration of heavy metals Hg, As, Cu, Pb, Cd, Cr and Zn in the sediment is 0.339 mg/kg, 14.815 mg/kg, 5.055 mg/kg, 3.436 mg/kg, 0.133 mg/kg, 12.667 mg/kg, 75.578 mg/kg, only Hg exceeded the quality standards of the first category of marine sediments. The concentrations of heavy metals in the surface seawater are higher in spring and summer, and higher in the sediments in autumn and winter, which is mainly related to the seasonal variation of runoff into the sea.The spatial distribution showed that the concentration of heavy metals in the core area of the Acipenser sinensis reserve was higher, and the Hg, As and Zn elements had an obvious enrichment trend. The comprehensive pollution index of heavy metals in seawater is greater than 5, which is at a serious pollution level, while the comprehensive pollution index of sediments is less than 5, which is at a low pollution level. The potential ecological risk coefficients of seven heavy metals are Hg > Cd > As > Cu > Zn >Pb> Cr. Except that Hg is at a very strong level of ecological risk, the other elements are at a low level of ecological risk. The comprehensive potential ecological risk index of heavy metals is at a strong level of risk.