Atherosclerosis (AS) is a chronic inflammatory disease with disorders of lipid metabolism. Metabolic disorders, inflammation and lipid deposition are prominent pathological features of atherosclerosis. Isorhynchophylline (IRN) has pharmacological effects such as protection of vascular endothelial cells, anti-inflammatory, anti-thrombotic, and anti-smooth muscle cell proliferation. However, it is unclear whether IRN is efficacious in atherosclerosis. In the present study, we verified the pharmacological efficacy and hepatoprotective effects of IRN in intervening in AS. LC-MS-based serum untargeted metabolomics was performed to search for potential biomarkers and related pathways in IRN-treated AS in ApoE-/- mice. Fifty-eight biomarkers were metabolically disturbed in the model mice compared to controls. Thirteen biomarkers showed optimal recovery methods after IRN-40 mg ml-1 intervention. We identified three metabolic pathways involved in IRN: glycerophospholipid metabolism, linoleic acid metabolism, and alpha-linolenic acid metabolism. These findings provide a research basis for the intervention of IRN in atherosclerosis.