Medium–high temperature geothermal systems with high fluoride contents are widely hosted in the Yingzhou–Xincun area of Lingshui, southeastern Hainan Island. However, the genetic mechanism of negative coupling between fluoride and salinity remains unclear, which restricts the refined exploitation of regional geothermal resources. In this study, multiple approaches including hydrochemical analysis, isotopic tracing and hydrogeochemical modelling were integrated to systematically investigate the genesis and spatial distribution of geothermal fluids from three geothermal fields in the study area. The main results are summarized as follows: (1) The geothermal system in the study area is a fractured granite geothermal reservoir developed in Mesozoic granites and controlled by the deep Jiusuo–Lingshui Fault. Geothermal fluids are recharged by meteoric precipitation from low hills in the northern part, with recharge elevations of 989–1128 m, groundwater residence ages of 3519-13304a, and reservoir temperatures ranging from 130 to 165°C. Reservoir temperatures exhibit a spatial pattern of higher values inland and lower values near the coast.(2) The maximum total dissolved solids (TDS) of geothermal water reaches 2600 mg/L, and the high salinity is not derived from modern seawater intrusion; TDS increases gradually from inland to coastal zones. Salinity is jointly controlled by deeply sequestered paleo-marine fluids and secondary soluble salts produced by silicate mineral leaching of granites. Cation exchange reactions further enhance the spatial differentiation of groundwater salinization.(3) Fluoride (F^-) concentrations in geothermal water range from 2.6 to 12.8 mg/L, showing a decreasing trend from inland to coast. Calcium ion activity is the dominant factor controlling fluoride enrichment, bicarbonate (HCO₃^-) acts as a secondary factor, and temperature exerts a synergistic promoting effect. Mixing of Ca-rich paleo-marine fluids triggers fluorite precipitation, which is the critical factor leading to low fluoride concentrations in coastal areas. This process ultimately results in significant negative coupling between F⁻ and TDS/Cl⁻ across the entire study area.(4) Combined with pumping test data and reservoir temperature calculation results, the study area is classified into high-temperature zones for geothermal power generation (Gaofeng and Hongxie) and medium-temperature zones for comprehensive geothermal utilization (Xincun). A zonal differentiated exploitation strategy and corresponding engineering protection schemes are proposed in view of the special hydrochemical characteristics of high fluoride, high salinity and high calcium.This study clarifies the hydrogeochemical mechanism responsible for negative fluoride–salinity coupling in coastal granite geothermal systems, fills the research gap of coastal granite geothermal systems on Hainan Island, and provides theoretical support for the sustainable exploitation of high-fluoride and high-salinity geothermal resources along coastal South China.