The waters of the Wanshan Islands are one of the traditional fishing grounds in China, but there is currently a lack of in-depth understanding of its fishery resources, particularly the reef fishery resources. Gillnetting and trawl surveys were conducted in the Wanshan Islands reef waters from March to April 2021, and the community structure, dominant species quantitative distribution, and diversity of fishery resources were analyzed. We captured 220 fishery species; 187 species were collected through gillnets and 52 species were collected through bottom trawl nets, affiliated with 16 orders, 72 families, and 137 genera, of which 176 species of fish and 38 species of crustaceans accounted for 80.0% and 17.3% of the total number of species, respectively. The index of relative importance (IRI) showed that the dominant species were Halichoeres nigrescens and Siganus canaliculatus in drift-net fishing and Trachurus japonicus, Leiognathus brevirostris, Thryssa kammalensis in trawl fishing, whose IRIs were higher than 1,000. The Shanon-Wiener diversity index (H′), Pielou evenness index (J′) value, and Margalef richness index (D) in gill net fishing were 2.50, 0.77, and 5.85, and in trawl fishing were 1.35, 0.54, and 2.52, respectively. The community characteristics of fishery resources have varying degrees of positive correlation with water temperature and silicate concentration. In general, the number and diversity of fishery resources found in the trammel net survey of Wanshan Islands is significantly higher than that of bottom trawl. The composition of fishery resources between the two survey methods is also quite different. Wanshan Islands are rich in rock fishery resources. However, there are fewer reef fishery resources with higher economic value.