Abundant geothermal waters have been reported in the Yalabamei, Zhonggu, Erdaoqiao, and Yulingong geothermal areas of the Xianshuihe Fault Zone of western Sichuan, southwestern China. This study focused on the hydrogeochemical evolution, reservoir temperature, and recharge origin of geothermal waters using hydrochemical and deuterium-oxygen (D-O) isotopic studies. Shallow geothermal waters represented by geothermal springs and shallow drilled water wells are divided into two hydrochemical groups: (1) the Ca–Na–HCO3 type in the Erdaoqiao area, and (2) Na–HCO3 in other areas. Deep geothermal waters represented by deep drilled wells are characterized by the Na–Cl–HCO3 type. The major ionic compositions of geothermal water are primarily determined by the water–rock interaction with silicate and carbonate minerals. The reservoir temperatures estimated by multi-geothermometries have a range of 63–150 °C for shallow geothermal water and of 190–210 °C for deep geothermal water, respectively. The δ18O and δD compositions indicated geothermal waters are recharged by meteoric water from the elevation of 2923–5162 m. Based on the aforementioned analyses above, a conceptual model was constructed for the geothermal system in the Xianshuihe fault zone.