Metabolomics is the systematic and comparative study of the levels of small-molecule metabolites in samples under various conditions. In biological system, metabolites play a critical role in a diversity of cellular functions. Metabolomics has been widely employed in toxicology and other fields. The purpose of this review is to summarize recent literatures on the application of LC–MS-based metabolomics in drug bioactivation and drug-induced liver injury (DILI) and to discuss their challenges in the field of toxicology. The emerging metabolomics could provide us a comprehensive view of novel biochemical sequelae in the cells, tissues, and organisms following toxicant administration. This article reviews LC–MS-based metabolomics in identification of biomarkers of drug toxicity and elucidating mechanisms of toxicity reported in recent years. This review also discusses the application of metabolomics combined with genomics or proteomics in the research field of DILI. LC–MS-based metabolomics has a great potential in drug metabolism, identification of biomarkers of cause and/or effect, and revealing the novel mechanisms of drug toxicity. In the future, metabolomics integrating with other omics can serve as an effective tool for investigating the mechanisms of drug toxicity.