Selenium, manganese, and calcium are necessary elements for maintaining normal growth and skeleton formation. Kashin-Beck disease mostly occurs in children, resulting in deformities, dwarfism, and disabilities. Selenium deficiency was considered a risk factor in China, while manganese was reportedly involved in it in Russia. Single-element regulation cannot be used in diagnosis because of unclear boundaries in patients compared to healthy individuals. In this study, new indices of elements were designed to predict the status of disease. MS (Mn/Se), CS (Ca’/Se), and MC (Mn/Ca’) values were designed, and prediction formulas were generated by comparing healthy children with those with Kashin-Beck disease via multiple linear regression analysis and discriminant analysis. In the disease group, 42.86% of patients had positive MS, CS, and MC values, and 57.14% of patients had positive MS and CS values. In the treatment group, the patients presented improved indices. In the prediction group, subjects with negative clinical criteria features were predicted by new indices, and 26.67% of them presented with positive MS, CS, and MC values, whereas 40.00% had positive MS and CS values. The 3D model of MS, CS, and MC refers to the setup of elements. The MS, CS, and MC indices are helpful in disease prediction, diagnosis, prognosis, and surveillance. The distribution model of the indices could serve in the growth surveillance of children.