Atherosclerosis, as the main root cause, makes cardiovascular diseases (CVDs) a substantial worldwide health concern. Inflammation and disrupted cholesterol metabolism are the primary clinical risk elements contributing to the onset of atherosclerosis. Few works exist on the improvement effect of gut microbiota on atherosclerosis. One specific probiotic strain, Enterococcus faecium NCIMB11508, has shown promise in mitigating inflammation. Consequently, it is critical to investigate its potential in reducing the progression of atherosclerosis. In our study, we administered NCIMB11508 orally to ApoE mice, resulting in a decrease in the formation of atherosclerotic lesions. Additionally, it demonstrated the ability to lower the inflammatory factor levels both in the aorta and blood serum while maintaining the integrity of the small intestine against lipopolysaccharides. Moreover, NCIMB11508 had a beneficial impact on the gut microbiota composition by increasing the levels of short-chain fatty acids (SCFAs), which in turn helped to reduce inflammation and protect the intestine. The probiotic NCIMB11508, according to our research, has a definitive capacity to prevent atherosclerosis progression by beneficially altering the SCFA composition in the gut microbiota of ApoE mice.