Understanding the relationship between fisheries resources and environmental factors, and also the spatial and temporal distribution of fisheries resources, plays an important role in the process of making fishery management and protection strategies. Under the policy background of “the Yangtze River Great Protection”, carrying out such research has an important ecological significance for fisheries protection and recovery in the Yangtze estuary. Based on the survey data from 2006 to 2017 in the Yangtze estuary, relationship between fish density and environmental factors was stusied based on GAM, meanwhile, the seasonal distribution of fish density in 2017 was predicted. The results showed that explained deviance in the seasonal optimal model was 69.6%, 55.9%, 51.4% and 47.4% respectively, and the mean slope of regression line of 100-time cross validation ranged from 0.62 to 0.88. Salinity, water temperature and dissolved oxygen (DO) were found to be the significant environmental factors. In general, in spring, summer and autumn, salinity was considered to have a positive relationship with fish density. In summer, autumn and winter, water temperature was found to be the significant environmental factor, and in Autumn, a positive relationship was found. In spring, autumn and winter, DO was found to be the significant environmental factor, and in winter, a positive linear relationship was found. In 2017, there was a relativelg high value of fish density in summer. In the four seasons, relatively low value of fish density was found to exist in the natural extension waters of the southern branch of the Yangtze estuary. In the natural extension waters of Chongming Island to the sea, the fish density is relatively higher.