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Cantharidin is the major bioactive compound extracted from the blister beetle, a traditional Chinese medicine, and has been proved to be a natural component with widely antitumor activity. However, clinical application of cantharidin is relatively restricted due to its potential toxic effects, especially hepatotoxicity. Although cantharidin-induced liver injury has been reported, the underlying molecular mechanisms remain unclear. In the present study, an UPLC-Q-TOF/MS based metabolomics approach combined with blood biochemical analysis, histopathological examination, and cell apoptosis assay were used to investigate the mechanisms of cantharidin-induced hepatotoxicity. A total of 54 significantly changed metabolites and 14 disturbed metabolic pathways were identified in the cantharidin exposed groups. Among them, four metabolites (oxidized glutathione, glutathione, 3-sulfinoalanine, and deoxycholic acid 3-glucuronide) were selected based on their high impact value and potential biological function in the process of liver injury post cantharidin treatment. Our study provides a deeper understanding of the mechanisms of cantharidin-induced hepatotoxicity and may contribute to reduce the liver injury and gain more effective and safe clinical use of cantharidin. In addition, our results also demonstrated that cantharidin could impair multiple biological processes in liver, and future studies will be necessary to reveal the detailed molecular mechanisms of cantharidin-induced hepatotoxicity.