The selenium (Se) poisoning, arsenic (As) poisoning and fluorine (F) poisoning have occurred in some areas of Ankang city in South Qinling Mountains which belong to the Eastern Qinling-Kunlun tectonic belt. In order to study the content of Se and other elements, water quality, health risks and utilization prospect in natural water of the Southern Qinling-Daba mountains, 77 natural water samples in Langao County, Ankang City, Shaanxi in South Qinling-Daba area. Additional 36 water samples from other major tectonic units in China were collected and analyzed with element contents for comparison. The results showed that the average concentration of Se (0.03–41.19 μg/L) in natural water is 7.93 μg/L (World is 0.2 µg/L), which have abundant natural Se-rich water resources. The hydrochemical type of natural water in Langao County of the Southern Qinling-Daba Mountain is mainly Ca–HCO₃⁻, and the water chemical composition is mainly controlled by carbonate rocks weathering. Higher concentration of Se, Mo and Cd of fissure water sample in Langao County, might be affected by Se-rich geological background, water–rock interaction, and less affected by environmental factors. The natural water in Langao County has a relatively low impact on human health and fissure water quality was good. The natural water in Langao County of South Qinling-Daba Mountain is pure and contains high contents of beneficial elements (especially Se and Sr), and this area has potential value for high-quality Se-type and Sr-type mineral water development. The study results are beneficial for water resources management in the mountainous area, and as a reference for relevant studies in other regions.