This paper was designed to study metabonomics characteristics of the hepatotoxicity and nephrotoxicity induced by JingDaJi (JDJ), a well-known traditional Chinese medicine which has been used for the treatment of scrofula, and as an antivirus and anti-inflammatory medication. Urinary samples from control and JDJ treated groups of rats were analyzed by ultra-performance liquid chromatography/mass spectrometry in positive ionization mode. Hepatic and renal tissues were histopathologically examined to identify specific changes occurring as a result of damage. The results suggested that the ethanol extract of JDJ (EJDJ) was responsible for the hepatotoxicity and nephrotoxicity that occurred following the ingestion of this medicinal herb. Using the principal components analysis, the levels of eight endogenous metabolites including creatinine, phenylacetylglycine, kynurenic acid, phenylalanine, leucine, hippuric acid, xanthurenic acid and 2,8-dihydroxyquinoline were found to be significantly changed in urine from EJDJ treated group. The formation of creatinine, phenylalanine, kynurenic acid, xanthurenic acid, leucine and 2,8-dihydroxyquinoline increased, while the biosynthesis of hippuric acid and phenylacetylglycine decreased.