We documented the data of fish species systematically collected in Southwestern Continental Shelf of Nansha Islands according to Nelson"s classification system and analyzed the diversity at different taxonomic levels using inclusion index at taxonomic level (TINCLi), taxonomic diversity (△ and ∧ ), relative abundances (R) and the similarity index (C) at order and family levels. The results indicated that the fish species in the Southwestern Continental Shelf of Nansha Islands belonged to 20 orders, 110 families and 206 genera, and Perciformes is the major order. Analyzed by the inclusion index at taxonomic level, the average number of (families, genera, species), (genera, species) and (species) in per order, family and genus are (5.5, 10.30, 14.85), (1.87, 2.70) and (1.44), higher than the case of East China Sea Continent Shelf, Daya Bay and Dongsha Islands at order level. The values assumed the inverse proportion with the variation of latitude which demonstrated that the taxonomic diversity of fishes in lower-latitude was lower than the higher-latitude. The average taxonomic distinctness △ and the variation in taxonomic distinctness ∧ of the Daya Bay were tested in this paper by the PRIMER5.2. The average taxonomic distinctness △ was 65.8, and the variation in taxonomic distinctness ∧ was 110.0. Compared the △ with those of East China Sea continent shelf, Daya Bay and Dongsha Island, the genetic relationship of the composition of fish species in Southwestern Continental Shelf of Nansha Islands was closer than East China Sea continent shelf (65.7) and farther than Dongsha Island(55.2) and Daya Bay(62.2). Compared the similarity index, at the order and family levels, the composition of fish species in Southwestern Continental Shelf of Nansha Islands is similar to the Daya Bay.