Amarogentin (AG) is a secoiridoid glycoside that is mainly extracted from the traditional Chinese medicine Swertia and Gentiana, which have been widely used in clinical practice to treat liver disease. However, the exact hepatoprotective mechanism of AG was still looking forward to further elucidation by far. In this study, C57BL/6 mice were divided into the following three groups: control, model and AG. Fibrosis was induced by CCl4. Mice were orally treated with 100 mg/kg AG or with normal saline as a control. At the end of the experiment, the validity of the model and the hepatoprotective effects of AG were examined by histopathology and biochemical indicators. Metabonomics technology was further performed to systematically evaluate the endogenous metabolite profiles. Gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) technology with pattern recognition analysis, including principal component analysis (PCA) and orthogonal partial least square discriminant analysis (OPLS-DA), showed a clear separation of the model group and the control group, with the AG treatment group located much closer to the control group than the model group, which was consistent with the results of biochemical and histopathological assays. Moreover, nine potential biomarkers were identified to elucidate the drug mechanism of AG, which may be related to pathways of amino acid and fatty acid metabolism.