Abstract: The Gongzhu Hot Spring, located in Biru County of the Xizang Autonomous Region, is currently under development, yet its hydrogeochemical characteristics and genetic mechanisms remain poorly understood. The key scientific questions concerning the lithology, temperature, and recharge and transport conditions of geothermal reservoirs in geothermal systems have not been fully resolved, hindering effective exploitation and sustainable utilization of the geothermal resources in this area. The study integrated field investigations with fluid geochemistry and isotopic testing to systematically analyse the hydrochemical characteristics and genetic mechanisms of the geothermal system associated with the hot spring. The results indicate that the geothermal water in the study area is mainly neutral to weakly alkaline, with a hydrochemical type of Cl—Na, belonging to immature water. Its chemical composition is mainly controlled by the dissolution of evaporite minerals and silicate minerals, as well as cation exchange. The geothermal water is mainly recharged by atmospheric precipitation. Based on corrected δD values, the calculated recharge elevations range from 5398 m to 5819 m, with a mean value of 5605 m. Tritium isotope analysis reveals geothermal water as a mixture of modern and ancient waters, characterized by prolonged residence time and distant recharge sources. Using the silicon enthalpy model method, the temperature range of the thermal storage is 183 °C−245 °C, and the cold water mixing ratio is 58.2%−89.8%, indicating a medium high temperature geothermal system. The geothermal system is recharged by precipitation in high mountain areas, which infiltrates through fractures in anticline trough zones, percolates to deep thermal reservoirs, and is heated through interaction with high-temperature rock masses or localized magmatic bodies. Due to pressure and density differences, heated groundwater migrates upward along the structural fracture zone to form hot springs on the surface. This study can provide valuable insights for the exploration and evaluation, scientific development, and sustainable utilization of geothermal resources in the Biru Area, Xizang Plateau.