Abstract: To investigate the distribution patterns of major reef-associated fish species in the waters of northern South China Sea (eastern Hainan Island) and their implications for marine ranching site selection, this study analyzed data from 12 bottom trawl cruises conducted in the northern South China Sea across five periods: 1963-1965, 1978-1979, 1997-1999, 2006-2007, and 2019-2023, respectively. Combined with 12 environmental factors, including sediment type, water depth, bottom water temperature, bottom salinity, nitrate, phosphate, silicate, dissolved oxygen, phytoplankton, primary productivity, underwater light intensity, and pH, the Maximum Entropy model (MaxEnt) was employed to simulate the suitable habitat distributions of five dominant reef-associated fish species: Pterois russelli, Trisotropis dermopterus, Tetrosomus concatenatus, Chaetodon modestus, and Daicocus peterseni. Key environmental drivers were also identified. The results showed that high-suitability habitats for the five dominant reef-associated fish species in the northern South China Sea were concentrated in the waters around eastern Guangdong-Pearl River Estuary region, at depths of 100-200 m with sandy-silty to silty-sandy sediments. The model exhibited extremely high predictive accuracy, with an average area under the receiver operating characteristic (ROC) curve (AUC) of 0.96. Phosphate, silicate, underwater light intensity, and sediment type were identified as the dominant factors influencing their distribution. Notably, sediment type indirectly regulates fish habitat and foraging behaviors by influencing nutrient cycling and the structure of the benthic community. This study provides the first validation of the limiting effects of phosphorus and silicon nutrients on the distribution of reef-associated fish in the northern South China Sea. A novel marine ranching site selection framework based on three principles, “ecological matching, nutrient buffering, and climate resilience” is proposed, breaking through traditional engineering-oriented site selection logic and offering new perspectives for fishery resource conservation and ecological ranching construction in the northern South China Sea.