Geothermal resources are the vital renewable energy for resolving energy crisis and environmental deterioration. Understanding hydrogeochemical processes, genesis mechanisms and scaling trends is crucial for securing the sustainable utilization of geothermal resources. In this study, fourteen geothermal waters were collected for hydrochemical and δ2H–δ18O isotopic analyses in northwestern Sichuan, SW China to clarify hydrogeochemical processes, genesis mechanisms, and scaling trends. Geothermal waters were recharged via atmospheric precipitation. Three different types of geothermal waters were identified using a piper diagram. Class 1 geothermal water with HCO3–Na and HCO3–SO4–Na types formed in the contact zone with Yanshanian intrusions and heated by residual radioactive heat. The hydrochemical processes were sodium/potassium silicate dissolution and positive cation–exchange. Class 2 geothermal water with HCO3–Ca and HCO3–Ca–Mg type was carbonate–type and heated by geothermal gradient. The dissolution of carbonate minerals dominated the hydrochemical process. Class 3 geothermal water with the SO4–Ca–Mg type was determined within deep faults. The dissolution of carbonatite and gypsum minerals and the oxidation of sulfides played a vital role in the hydrochemical process. The reservoir temperatures of geothermal waters followed the orders of Class 1 (74.9–137.6 °C) > Class 3 (85.9–100 °C) > Class 2 (38.7–93.5 °C). Calcium carbonate scaling should be paid attention to in Class1 and Class 3 geothermal water, and calcium sulfate scaling merely occurs in Class 3 geothermal water. This study provides vital information for geothermal exploitation in western Sichuan and other similar areas.