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Metabolic syndrome is a chronic systemic metabolic disorder. The number of patients with this disease is increasing year by year, and its prevalence is affected by age, gender, and dietary habits. Studies have pointed out that metabolic syndrome is closely related to insulin resistance, obesity, oxidative stress, and inflammation. In recent years, it has been found that intestinal flora is closely related to metabolic syndrome through omics methods such as macroeconomics and amplicon sequencing. Probiotics, a strategy to regulate intestinal flora, can improve oxidative stress, reduce the secretion of pro-inflammatory factors, and regulate glucose and lipid metabolism by regulating intestinal flora and its metabolites, thereby alleviating metabolic syndrome. This article systematically summarizes the pathological mechanism of metabolic syndrome and the relationship between intestinal flora and metabolic syndrome, and expounds the key molecular targets and specific signaling pathways by which probiotics mitigate metabolic syndrome. This review hopes to provide a theoretical reference for the development of probiotics as a new strategy for the treatment of metabolic syndrome and the targeted mining of healthy and functional microorganisms with the ability to improve metabolic syndrome.