We performed a fixed-point survey in the southwestern sea of the Nansha Islands (SS) and the mouth ofBeibu Bay (SN) in the South China Sea from 2012 to 2013. Catch species composition, the index of relative importanceof each species, the Margalef richness index, the Shannon-Weiner diversity index, the Pielou evennessindex, and the relative density of resources were calculated. We identified 663 species in four classes, 36 orders,171 families, and 374 genera from catch resources in researched areas of the South China Sea. A total of 504 fishspecies were detected, which accounted for 76.0% of the catch. The number of dominant species in autumn washigher than that in spring, and the number of species captured in the SS was higher than that caught in the SN,with obvious seasonal fluctuations. All diversity indices were higher during the spring than those during the autumnbecause supplemental groups occurred in spring and many species moved to deep sea in autumn. However,all diversity indices in the SS were higher than those in the SN owing to greater effects of sea temperature andcurrents in the SS. Fisheries resources in the northern South China Sea were highly overfished, making the fisheryresource smaller compared with historical fishery resource data. Fisheries resources in the SS were supposed to bereasonably exploited under nationally supported policies with better relative stock density. Stability of the SouthChina Sea fishery is based on high species diversity; therefore, it is important to reasonably exploit the fisheriesresources while protecting species diversity.