Atherosclerosis is a chronic metabolic disease in which lipids and complex carbohydrates are deposited on the inner wall of large and medium arteries. Its pathogenesis is complex and affected by various risk factors, and it is the main pathological basis of cardiovascular disease. Recent studies showed that the gut microbiota can affect the process of atherosclerosis through various mechanisms, including regulating host metabolism and inflammation. Maintaining the dynamic balance of the intestinal flora through dietary interventions, probiotics, prebiotics, and fecal-bacteria transplantation can effectively delay the progression of atherosclerosis. Among these approaches, next-generation probiotics, including Akkermansia muciniphila, Christensenia minuta, Faecalibacterium prausnitzii and other non-traditional intestinal flora and gene-edited designer probiotics, have become new prevention and treatment tools. The gut microbiota thus presents a potential diagnostic and pharmacological target for the prevention and treatment of atherosclerosis.