Abstract: The Red River Fault Zone in western Yunnan is endowed with abundant geothermal resources. Systematic investigations of its geochemical signatures and genetic mechanisms are essential for the sustainable development and utilization of regional geothermal energy. Multi-media geochemical surveys with machine learning approaches—including a coupled self-organizing map and K-means (SOM-KM) clustering model and Mantel test-validated positive matrix factorization (PMF) modeling, were employed to elucidate the response of geothermal fluids and associated travertine deposits to deep hydrothermal processes. The results demonstrate that SOM-KM clustering effectively distinguishes the dominant factors controlling the formation and evolution of geothermal fluid chemistry. Quantitative source apportionment identifies five primary processes governing fluid solute compositions: evaporite dissolution and mixing with paleo-saline water within fault-bounded basins (38.05%), carbonate dissolution coupled with high-temperature decarbonation (23.50%), atmospheric precipitation, surface water, and shallow groundwater recharge (19.41%), water-rock interaction with silicate rocks (9.76%), and upwelling of deep primary geothermal fluids (9.28%). Notably, geothermal fluids in the Eryuan Niujie–Sanying Basin exhibit geochemical affinities with mid-ocean ridge hydrothermal systems, driven by intensive water–rock interactions with oceanic island tholeiites and pelagic hydrothermal carbonates. Such geochemical characteristics are consistent with the alkaline high-temperature fluids of the Tengchong Rehai geothermal field, indicating fluid origins dominated by deep crustal circulation rather than direct magmatic input. Collectively, geochemical evidence confirms that the typical geothermal systems along the Red River Fault are non-magmatic, deep-circulation hydrothermal systems. The geothermal accumulation models can be classified as deep-circulation convective type in uplifted mountainous fault zones, and convective-conductive composite type in fault-depression basins. The thermal regime is characterized by a layered heat convergence mechanism involving mantle-derived heat supply at depth, frictional shear heating along fault planes, convective heat transfer in shallow aquifers, and radiogenic heat production within concealed intrusive and metamorphic crystalline basements. Estimated reservoir temperatures in this region range from 61.89 ℃ to 186.40 ℃, with circulation depths varying between 1 231.67 m and 6 308.35 m. Furthermore, the core segment of the Ailaoshan-Red River Fault Zone, characterized by extensive Cenozoic potassic magmatism and lithospheric delamination, provides favorable structural conditions for deep fluid infiltration and circulation. Intersections between primary faults, secondary branch faults, and extensional rift-basin faults are highlighted as high-potential targets for medium- and high-temperature geothermal exploration.