Introduction: 'Renqing Mangjue' pill (RMP) is a classical and empirical clinical prescription of Traditional Tibetan Medicine (TTM), but the absence of the mechanism of action restricts its clinical application. We aimed to explore the toxicological effects of RMP. Materials and methods: The dose-dependent perturbations in urinary metabolite concentrations caused by RMP toxicity were investigated using 1H NMR spectroscopy coupled with multivariate statistical analysis. Wistar rats were investigated by exposing to RMP at different dosages. Urine samples were collected during toxic insult and regenerative phase and analyzed by NMR, ICP-MS and multivariate data analysis. Partial least squares-discriminant analysis (PLS-DA) of 1H NMR from rat urine revealed a dose-dependent metabolic shift between the vehicle-treated control rats and rats treated with RMP. Results: Compared with control group, the administration of high dosed RMP led to elevation of urinary carnitine, cysteine, alpha-ketoglutaric acid, tyrosine, alpha-hydroxy-n-valerate and 4-aminohippurate accompanied by level decreases in urinary creatinine, glucose, histidine, lactate and urocanate in 1 day post-dose. After 15 days following the administration of high dosed RMP, the higher concentration of creatinine, cysteine, glucose, asparagine, allantoin, isoleucine and glutamate and the lower concentrations of histidine, tyrosine, tryptophan and urocanate were observed. Conclusion: The toxicity involves the perturbation of energy metabolism, amino acids metabolism and purine metabolism in high dosed group, while changes in another two dosed groups were less significant. An immediate As-related toxicity was also observed in high dosed group. Hg and Pb may be responsible for the inhibition of the recovery since they could not excrete easily from urine. This work illustrated the high reliability of NMR-based metabonomic approach on the study of the biochemical effects induced by traditional Tibetan medicine.