This study probe the human health risk of fluoride (F), arsenic (As), and selenium (Se) and their daily intake available quantity to human through different sources in different regions of Shaanxi, China. For this purpose, a number of samples, including coal and coal wastes, rocks, soil, and vegetables were collected from south Qinling Mountain stone-like coal (Geo type-I), Binxian-Jurassic (Geo type-II), Hancheng Permo-Carboniferous (Geo type-III), and countryside (Huanglong County) of Shaanxi province. All these samples were analyzed through atomic fluorescence spectroscopy and combustion hydrolysis methods. Results showed that Geo type-I was enriched with As, Se, and F, Geo type-II, III, and the countryside were slightly enriched with As and F and deficient in Se. The average daily intake (ADI) of Se in Geo type-I was 0.005-0.0045, Geo type-II 0.0005-0.0004, Geo type-III 0.0006-0.0005, and countryside 0.0002-0.001 in mg kg^-1 day^-1 adult-children, respectively, which was lower than the optimum level (0.06-0.075 mg kg^-1day^-1). ADI of As at Geo type-I was 0.0085-0.0075, Geo type-II 0.004-0.0037, Geo type-III 0.0008, and countryside 0.00022-0.00019 in mg kg^-1 day^-1 adult-children, respectively, which was above the acceptable range (10^-6-10^-4). ADI of F at Geo type-I was 0.0047-0.0041, Geo type-II 0.0098-0.0087, Geo type-III 0.002-0.0017 and countryside 0.0015-0.0013 in mg kg^-1 day^-1 adult-children, respectively. The toxicity level of Se and F at all the regions was lower than the NOAEL and LOAEL, while As was higher at Geo type-II and I. The extreme deficient of Se than the optimum range along with high F could deregulate the normal body growth especially causes bones and joint problems. However, the study found a rare patient with bone and joint disease (maybe Kashin-Beck disease) in the countryside. To find the exact cause of Kashin-Beck disease, the study needs further medical investigation in Se-deficient regions and their association with selenium deficiency and enriched fluoride.