studing the effect and mechanism of variability of habitat factors on important biological resources in the Yangtze River estuary (YRE), we evaluated the relationship between fish community structure and environmental factors in the YRE. We collected fish by bottom trawling and obtained environmental data from 30 stations in the YRE in May and June 2010. In addition, we used historical data to analyze the effect of large hydraulic projects on fish community dynamics in the YRE. We collected a total of 40 fish species belonging to 23 families and 12 formers. The Engraulidae and Gobiidae families were the most abundant (5 species each), followed by Sciaenidae (4 species), and Cynoglossidae (3 species). The trawl catches were dominated by young-of- year juveniles. The most abundant species (94.11% of the total catch) by life history type were (marine migrant), (anadromous). Cluster and non-metric multidimension scaling analysis revealed significant spatial variation in the fish community. Of the nine environmental variables we measured, water depth, bottom salinity, and surface salinity were the most significant factors influencing fish species richness and density in the inner zone. Conversely, the fish community in the outer zone was primarily influenced by the bottom pH, surface salinity, and bottom temperature. The number of fish species declined compared to historical catches in May (69 species, 1.72×10⁴ ind/km²)and June (62 species, 2.29×10⁴ ind/km²) in 1985, though fish density (5.2×10⁴ ind/km²) increased. Our results indicate the YRE has still been the spawming and nursery ground for commercial species, but fish community structure has varied.