Herein we investigate the species composition and taxonomic diversity of coral reef ecosystems in a typical small-scale area in Qilian in the Xisha Islands. Based on fish survey data from the Nanhai Qilian Islands fishery in the 1970s and 2018-2019, we summarized the species composition of the Qilian Islands reef fish species using the taxonomic diversity index and the (family) diversity measure index. We found that the reef fish in the Qilian Islands area belonged to 175 species of 70 genera, 33 families, and 8 orders. Perciformes accounted for the largest percentage, at 81%. The average classification difference index (Δ⁺) is about 54.19, and the classification difference variation index () is about 112.35. We compared the community composition of Qilianyu fish to different regions, both at home and abroad. We found that the Δ⁺ of the Qilianyu fish is lower than the East China Sea shelf, Daya Bay, and Yubi Reef, but was higher than the Qibi Reef. The average grade-of-diversity index (-index) average was 3.09 and the normalized index average was 0.40. The results indicate that the classification of species in the fish community of Qilianyu is higher, and the genetic relationship is closer, than that of the East China Sea shelf, Daya Bay, and Zhubi Reef. The index values indicate that the species diversity of the reef fish in Qilianyu is relatively high, and that the distribution of families and genera was good historically. However, in 2018-2019, the diversities of the family and genus decreased significantly, so it is suggested to protect them in time.