Geothermal energy is a vital renewable resource widely used for various applications, including drinking water, domestic supply, irrigation, and industrial purposes. However, the utilization of geothermal water for drinking can expose individuals to toxic elements, particularly arsenic, which poses significant health risks. Despite the growing interest in geothermal water, there has been a lack of systematic analysis regarding the spatial variability of its quality and health risk. This study aims to address this gap by evaluating the spatial variability of the water quality characteristics and health risks in Yunnan Province using a combination of hydrochemical and isotopic methods, Principal Component Analysis (PCA), Self-Organizing Maps (SOM) and integrated tools such as Water Quality Index (WQI) and Human Health Risk Assessment (HHRA). According to this study, atmospheric precipitation serves as the primary recharge source with Na-HCO3, Ca-HCO3, Na-Cl and Ca-Cl as the dominant geothermal water hydrochemical in Yunnan Province. While most samples exhibit good water quality, those from the northwestern regions (e.g., Lijiang, Lincang, Kunming, Baoshan, Jinghong, Pu'er, and Dali) show poorer water quality and significant health risks. PCA analysis reveals that the spatial variability of geothermal water quality is largely influenced by deep hydrological cycles and magma-tectonic interactions, resulting in arsenic enrichment in high-risk areas. This study addresses the research gap regarding the spatial variability of geothermal water quality and health risk assessment in Yunnan Province and provides a scientific foundation for sustainable development and management.