In order to ascertain the fish community structure in the southern waters of the Yangtze River Estuary， 12 stations were set up in the North Port， the North Channel and the South Channel of the Yangtze River Estuary in April （spring） and September （autumn） of 2020， and two voyages of fishery resource surveys were conducted using single bag trawls （minimum mesh size 25 mm）. By calculating individual， weight resource density， relative importance index， α-diversity index， combined with multiple factor regression analysis and canonical correspondence analysis （CCA）， we could determine the spatio-temporal change rule of the community and the impact of environmental factors on the distribution. In this study， 49 species of fish were collected， belonging to 16 orders， 25 families and 41 genera. All of them are warm temperature and warm water fish. The majority of them are estuarine fish， while the narrow salt fish are less and distributed regionally. The resource density in spring is higher than that in autumn， while the weight resource density in autumn is higher than that in spring. Coilia mystus， Coilia nasus， Collichthys lucidus and Miichthys miiuy were dominant species in both seasons. In spring， Miichthys miiuy's individual resource density has the highest contribution rate to the total density and the most significant impact. In autumn， the contribution rate of the individual resource density of Harpadon nehereus is the highest， but the influence of the individual resource density of Coilia nasus is the most significant. The results of individual and weight diversity index showed that H'， J' and D' in autumn were higher than those in spring， while the average value of C' in spring was higher. The surface salt temperature of the water surface in the study area is affected by many dynamic factors and there is a large seasonal change. The resource density plane distribution map and the ranking map reveal that certain groups have a life habit of tending to temperature and salt.