Based on the data collected from the bottom trawl survey and environmental investigation in November 2014 and May 2015, this paper studied the community structure of fish assemblage and its relationships with 6 major environmental factors in Sanmen bay. The results show, a total of 33 fish species were captured, species composition was dominated by seasonal migratory species, the settling species played a leading role in biomass, and the species were mainly composed of warm water fishes. There were 5 kinds of dominant species in autumn and spring, Collichthys lucidus, Harpodon nehereus, Trypauchen vagina were the common dominant species; NMDS and ANOSIM analysis revealed that the survey stations could be divided into 2 groups, of which one group was mainly distributed on the inside of the bay and the other one was mainly in the estuary; Significant difference was detected between the different stations in each season; The size spectrum analysis showed that the slope and intercept of fish community structure have obvious seasonal differences in Sanmen bay. RDA analysis showed that the fish communities structure was dominated by environmental factors such as temperature, dissolved oxygen, suspended matter and pH.