Radix Bupleuri (RB), with a Chinese name Chaihu, is one of the most popular Traditional Chinese herbal drug. It can be baked with vinegar to afford vinegar-baked Radix Bupleuri (VBRB), which is used in Traditional Chinese Medicine (TCM) for liver diseases treatment. In the present study, nuclear magnetic resonance-based metabolomic approach was used to compare the liver protective effect of RB and two types of VBRBs, which were prepared by two kinds of vinegar. The contents of 14 metabolites in the liver of carbon tetrachloride (CCl4) treated mice were significantly altered in comparison with control group, and VBRB prepared by Shanxi vinegar showed best effect as revealed by the amount and regulatory degree of the perturbed metabolites. The metabolism pathways analysis showed that the liver protective effect was related with the energy metabolism, lipid metabolism, ketone body metabolism, glutathione metabolism, amino acids metabolism and nucleotide synthesis. The results presented here showed that metabolomic approach made it possible to disclose the subtle biological difference between two types of VBRB, which highlight the potential of metabolomic approach to quantitatively compare the pharmacological effect of the herbal drugs.