To study the fish community structure in islands area, a fishery-independent survey was conducted in August and December of 2016, February and May of 2017. The cluster analysis, nonmetric multidimensional scaling (nMDS) and biological environment correlation analysis (BIOENV) were used to study the composition of fish community in our study area. A total of 96 species were collected, which belonged to 77 genera, 47 families and 12 orders. The Perciformes has maximum ratio, which accounted for more than 50% of their biomass and abundance. Harpadon nehereus was the dominant species throughout the year. In addition, the dominant species in spring were Psenopsis anomala, Collichthys niveatus, and Cynoglossus robustus; the dominant species in summer were Larimichthys polyactis, Trichiurus lepturus, and Chaeturichthys hexanema; the dominant species in autumn and winter were Collichthys lucidus and Coilia mystus. The fish community in the Ma'an Archipelago and its eastern waters can be divided into group I (the sites sorrounding island and reef), group Ⅱ (the sites adjacent to reef), and group Ⅲ (the sites far off island and reef). There were significant differences in species composition between groups, and seasons (R=0.651~0.977), except the spring group I and group Ⅲ, group Ⅱ and group Ⅲ. BIOENV analysis showed that the bottom water temperature had the most significant impact on the fish community compared to bottom salinity and water depth.