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Polycystic ovary syndrome (PCOS) is one of the most common endocrine metabolic disorders in women of childbearing age, characterized by hyperandrogenemia, polycystic ovary, sparse ovulation or anovulation. PCOS features high incidence, complex phenotype, and unclear etiology and pathophysiology. In recent years, many studies have focused on the role of the human microbiome in the pathophysiology of PCOS. Therefore, this review focuses on the interaction of PCOS with the reproductive tract microbiome and the gut microbiome, and summarizes the characteristics of the microbiome of PCOS patients, how PCOS affects the human microbiome, and the role of the human microbiome in the development of PCOS.