BACKGROUND: Apolipoprotein M (ApoM), a protein component of lipoproteins, is closely related to the development of atherosclerosis, but the specific mechanism remains elusive. Mitochondrial DNA damage can contribute to atherosclerosis, so this study was designed to investigate whether ApoM influences the structure and function of mitochondria during the progression of atherosclerosis and to explore the underlying mechanism. METHODS: Atherosclerosis models were established in male ApoM-deficient ( RESULTS: In CONCLUSIONS: ApoM exerts atheroprotective effects by promoting autophagy and regulating mitochondrial dynamics, thereby maintaining mitochondrial integrity and function. This study provides novel insights into the mechanisms underlying the protective role of ApoM in atherosclerosis and highlights its potential as a therapeutic target for cardiovascular diseases.