Geothermal energy resources are abundant in the Qinghai Gonghe Basin. Helium isotope evidence indicates that the heat source of the high-temperature geothermal system of the basin is the crustal overlying melt, but the genesis of the melt is still unclear. The composition of 87Sr/86Sr, δ2H, and δ18O confirms that the hot water in the basin is recharged by atmospheric rainfall from the surrounding peaks at an elevation of 3500–5500 m. Based on a comparison with typical mantle-source thermal areas such as Yellowstone Park and Yangbajing, we found that the hot spring water of the Gonghe Basin is peripheral, not steam-heated or mantle-source. Na, K, and Mg composition shows that the reservoir temperature ranges from 140 to 240 ℃, indicating great resource potential. Rare gas isotopes indicate that only about 5% of the basin heat comes from the mantle. The numerical simulation found that the rapid uplift in local areas of the basin made the granite with high thermal conductivity exposed to the surface, resulting in a thermal refraction effect and local thermal anomaly. According to the results of this study, the high-temperature geothermal resources in the Gonghe Basin may not be evenly distributed throughout the whole basin, but in stripes concentrated in areas associated with tectonic uplifting, such as the eastern side of the South Mountain of Qinghai and the eastern and western sides of the Waliguan Mountain.