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Compared to the southern Tibetan Plateau, the northern part has been regarded as relatively lacking geothermal resources. However, there is no lack of natural hot springs exposed in beads along large-scale fracture systems, and research on them is currently limited to individual hot springs or geothermal systems. This paper focuses on the Wahongshan-Wenquan Fracture Zone (WWFZ), analyzes the formation of five hydrothermal activity zones along the fracture zone in terms of differences in hot water hydrochemical and isotopic composition, and then explores the hot springs’ hydrothermal control in the fracture zone. The results show that the main fractures of the WWFZ are the regional heat control structures, and its near-north–south- and near-east–west-oriented fractures form a fracture system that provides favorable channels for deep hydrothermal convection. Ice and snow meltwater from the Elashan Mountains, with an average elevation of more than 4,500 m above sea level, infiltrates along the fractures, and is heated by deep circulation to form deep geothermal reservoirs. There is no detectable mantle contribution source heat to the hot spring gases, and the heat source is mainly natural heat conduction warming, but the “low-velocity body (LVB)” in the middle and lower crust may be the primary heat source of the high geothermal background in the area. The hot springs’ hydrochemical components show a certain regularity, and the main ionic components, TDS, and water temperature tend to increase away from the main rupture, reflecting the WWFZ controlling effect on hydrothermal transport. In the future, the geothermal research in this area should focus on the hydrothermal control properties of different levels, the nature of fractures, and the thermal contribution of the LVB in the middle and lower crust. Full article