Abstract: Aiming at the prominent contradiction between aquaculture and ecological protection, as well as the saturation of inshore aquaculture space in the island and reef waters of the South China Sea, this study aimed to clarify the potential habitat distribution characteristics and key regulatory factors of indigenous representative aquaculture species, so as to provide scientific basis for the optimization of aquaculture layout and the construction of marine pastures in this region. Eleven indigenous aquaculture species (3 shellfish, 1 shrimp, and 7 fish) in the island and reef waters of the South China Sea were selected. Species distribution data and 48 marine environmental variables were integrated, and 21 core variables were retained after multicollinearity screening. Combined with the MaxEnt model and ecospat model, the distribution of potential suitable habitats for the species was simulated, the contribution rates of key environmental factors and the degree of interspecific niche overlap were quantified, and a comprehensive suitability evaluation was conducted based on 12 potential aquaculture sites around Naozhou Island. The results showed that the constructed species habitat models performed excellently: the AUC values of the training set for all 11 species were > 0.9; in the test set, only the AUC value of Penaeus japonicus was 0.898 1 (good), while the others were > 0.9 (excellent). Water depth, distance to land, and wave height were the core physical factors dominating the distribution of most species (contribution rate: 35.19%-65.42%), and nutrient and temperature factors showed species-specific effects. The niche overlap of shellfish was low (Schoener's D=0.178 0-0.387 1), while some fish species had high niche overlap (D>0.5). The waters around Naozhou Island were the core aquaculture areas for Babylonia areolata, Larimichthys crocea, and Trachinotus ovatus, and multi-species co-culture could be realized at some sites in the eastern part. This study clarified the habitat suitability parameters and differentiation rules of indigenous aquaculture species in the island and reef areas of the South China Sea, and identified the dominant regulatory role of physical environmental factors. The results provide quantitative support for the precise selection of aquaculture areas and the eco-friendly layout.