To understand why Procapra przewalskii does not show the same white myopathy as sheep in Se-deficient regions and to provide reference for feeding nutrition level of artificial population and selection of wild reintroduction areas in the later period, a Se-deficient model was established. The mineral elements content, physiological and biochemical parameters in blood and serum metabonomics were determined. In the Se-deficient group compared with the control group, the Se content was highly significantly lower (P < 0·01), and the Cu content was significantly higher (P < 0·05). The activity of glutathione peroxidase was significantly lower (P < 0·05), but total superoxide dismutase was significantly higher (P < 0·05). By matching the mass spectrum data of compounds with the Kyoto Encyclopedia of Genes and Genomes (KEGG database), eighty-six types of differential metabolites in the serum were identified. The main metabolic pathways included secondary bile acid biosynthesis, biosynthesis of unsaturated fatty acids and pyrimidine metabolism. Further analysis showed that there were seven different metabolites in pyrimidine metabolism pathway between the two groups. And there was no significant difference in erythrocyte, Hb and total antioxidant capacity between the two groups (P > 0·05). The above results showed that the differential metabolism of substances exhibited complementary functions, thus alleviating some adverse effects and resulting normal activities of P. przewalskii can be carried out under the condition of dietary Se content lower than 0·05 mg/kg.