The southern coastal waters of Wenzhou is in the mid to southern parts of the East China Sea. This area is influenced by the high temperature and high salinity conditions of the Taiwan Warm Current, the low salinity of the Zhejiang Coastal Current, and the southern coastal upwelling. These waters are rich in nutrients and baitfish and are highly diverse with fish species. The area is a typical ecological region of the East China Sea shelf. Cluster analysis, non-metric multidimensional scaling, and a diversity index was used to analyze the patterns of community composition, diversity, and community structure based on data from two fishery resources investigations conducted in May (spring) and September (autumn) 2015 in the area. The results identified 47 species in the southern coastal waters of Wenzhou, which belonged to 41 genera, 27 families, nine orders, and two classes. Warmwater and warm temperate species were dominant, and Perciformes were the most abundant, with 26 species, followed by Clupeiformes, with six species. The third most frequent group was Tetraodontiformes, with four species. The dominant species in spring were Amblychaeturichthys hexanema, and , accounting for 49.3% of the total catch. The dominant species in autumn were Polynemus sextarius, accounting for 50.8% of total catch. , were typically found at all stations in both seasons, and they were the major divergent species causing community differences among stations. Pearson's correlation analysis indicated that the richness index () were positively correlated with dissolved oxygen, salinity, and temperature. A canonical correspondence analysis suggested that the main environmental factors affecting the spatial patterns of fish assemblages were pH, depth, and salinity. pH represents the sum of some of the chemical properties in water and is the result of interactions among factors. pH can be affected by salinity and temperature. The canonical correspondence analysis results showed a division in the fish community in spring, which was likely due to influx of the high temperature and high salinity water in the Taiwan Warm Current. This current forms an obvious salinity gradient in the local coastal strip, which further affected the division of the spring fish community. The Taiwan Warm Current retreated in autumn, and the lower temperature and lower salinity of the Zhejiang and Fujian Coastal Currents gradually carried a large amount of silt into the study area. Therefore, whether temperature, salinity, and suspended particles affected the fish community structure requires further investigation.