The southern Yellow Sea shows complex ocean-current and hydrological features, which caused complex spatial structure of fish assemblages that have been poorly understood. Based on seasonal bottom-trawl survey data collected from 2014 to 2015 in the coastal waters of southern Yellow Sea, we used multivariate methods to analyze the structure of fish assemblages, and compared the biomass, diversity, and dominant species among faunas. The results of Cluster and MDS showed that fish assemblage in the southern Yellow Sea could be divided into the Haizhou Bay fauna and the coastal waters of Jiangsu Province fauna. The fish assemblage in Haizhou Bay showed higher species biodiversity and average catches than those of the coastal waters of Jiangsu Province, whereas the relative biomass of warm-water and warm-temperate species in Haizhou Bay community was lower than the other. The dominant specie were Pholis angi, Hexagrammos otakii and Engraulis japonicas in Haizhou Bay with significant seasonal alternations, while they were Collichthys lucidus, Miichthys miiuy, Cynoglossus joyneri and Collichthys niveatus in coastal waters of Jiangsu Province with trivial changes. Our study demonstrated that fish assemblage in the southern Yellow Sea could be divided into two faunas with significant differences in fish assemblage structure, which were attributed to the different water masses, ocean currents, depth and bottom sediment types in the two regions.