Objective To evaluate and discuss the changes of biomarkers of abnormal Savda syndrome rat model in Uyghur traditional medicine by external feature observation and urine metabolomics assessment. Methods The abnormal Savda syndrome rat model was established according to the theory of Uyghur traditional medicine. Its external characteristics such as hair, tongue, sleep, feces, emotion and weight growth rate were observed and scored, and their urine was detected and analyzed by proton nuclear magnetic resonance (¹H-NMR) spectroscopy. Results Compared with the healthy control group, there were significant changes in the external features in the abnormal Savda syndrome rat model group, including dry and hard stools, reduced urine output and darker color, dry fur, dark purple tongue with ecchymosis, and decreased weight growth rate. Moreover, 23 urinary metabolites were significantly reduced, including propionate, lactic acid, pyruvic acid, acetic acid, alanine, acetamide, glycoprotein, acetone, methyl guanidine, sarcosine, ornithine, glycine, creatine, creatinine, aminoanhydride, β-galactose, urocanate, tyrosine, phenylalanine, hippuric acid, aminohippuric acid, formic acid and lysine. However, urea, citric acid, allantoin and α-ketoglutaric acid were significantly increased. Conclusions During the development process of Savda syndrome, there are not only abnormal changes in external appearance in the model rats, but also evident changes of many internal metabolic pathways. The obvious abnormalities of the urine metabolites may be related to the biological mechanisms of abnormal Savda syndrome.