Hot springs in fault zones play a critical role in studying the structural effects on the evolution of geothermal systems. The northern Red River Fault Zone lies in the western part of Yunnan, southwest China, with hot springs ranging from low-medium to high temperatures. From 2013 to 2019, thirty water samples were collected to analyze hydrochemical characteristics and structural effects. The hydrochemical compositions of hot springs mainly come from the weathering or dissolution of the carbonate, evaporite, and silicate minerals, and the cation exchange. High contents of F and Si in the hot springs of high temperature enhance water–rock interactions. For hot springs along faults, there is a positive correlation between TDS and circulation depth. Li/Cl ratios show that geothermal waters have three reservoir sources of different depths. Hot spring waters from shallower reservoirs are mainly Ca-SO4 or Ca-HCO3 type, and those from deeper reservoirs are Na-HCO3 type. Hydrochemical compositions of the hot springs are controlled by faults in terms of circulation depth and geothermal reservoirs. Hot spring waters are mixed, with the proportions of cold water ranging from 60% to 90%. The hot springs with varying mixing ratios may indicate the heterogeneity of fault networks and different reservoir sources. This study underlines the hydrochemical evolution of geothermal water along faults, with key implications for the understanding and exploitation of geothermal systems in the fault zone and similar regions.