Paeonol extracted from the Moutan Cortex, possesses hepatoprotective activity against epirubicin (EPI)-induced liver damage. This study evaluated the protective effect of paeonol on EPI-induced hepatotoxicity and explored the underlying metabolomic mechanism. Breast tumor-bearing mice were randomly divided into three groups: control, EPI, and EPI + paeonol treatment. Mice received a tail i.v. injection of EPI every other day for 3 cycles or/and intragastrically (i.g.) administered paeonol daily for 6 days. Hematoxylin-eosin (HE) staining and biochemical detection were used to determine the degree of damage. A gas chromatography-mass spectrometry (GC-MS) technique was established to determine the metabolites. PLS-DA and PCA were used to investigate metabolic changes. HE staining and biochemical detection results showed that EPI caused serious liver damage while paeonol ameliorated it. The results of mass spectrogram, partial least squares-discriminate analysis (PLS-DA), and principal component analysis (PCA) demonstrated that lipid, amino acid, and energy metabolism involving seven metabolites were obviously changed by EPI and reversed by paeonol. Additionally, paeonol inhibited EPI-induced activation of adenosine monophosphate activated protein kinase/mammalian target of Rapamycin (AMPK/mTOR) signalling pathway. Our results demonstrated the hepatoprotective effect of paeonol on EPI-induced hepatotoxicity in mice, provided potential biomarkers for early assessment of EPI-induced liver injury and illuminated the metabolic mechanism underlying paeonol-related hepatic protection.