Geothermal resources are abundant, widely distributed, and environmentally friendly as a renewable energy source, making their utilization and genesis studies highly significant. In the Tibet's Ali region, geothermal potential is considerable but development is limited. Based on hydrogeochemical data from 15 geothermal sampling sites and 2 cold-water sampling sites, this study analyzes the formation and evolution of regional hot spring waters. Results show that the hot springs are predominantly of the HCO3–Na type, with other water types, including HCO3·Cl–Na and HCO3·SO4–Na. The hydrochemical composition is controlled by the dissolution of silicate minerals, weathering of evaporites, and cation exchange. Water–rock interactions cause enrichment of trace elements, such as B, I, and Li, and their mobility reflects a complex multiphase recharge system with varied hydrogeodynamic processes using the silica–enthalpy method to estimate the original reservoir temperature ranges from 173.1 to 266.3 °C. As the geothermal fluids ascend, mixing with cold water accounts for 59–93%. The mixed temperatures range from 58.22 to 135.43 °C. Hydrological and geochemical indicators suggest that Zone II exhibits strong system enclosure, long fluid residence time, and slow runoff; Zone III shows moderate enclosure with secondary water–rock interactions; Zone I represents an open circulation with rapid groundwater recharge. This study provides scientific basis and guidance for understanding the genesis of Ali hot spring waters and the sustainable development of regional geothermal resources. However, limitations include a lack of isotopic constraints and insufficient sampling spatial resolution, which should be addressed in future research.