Polycystic ovarian syndrome (PCOS), characterized by chronic anovulation and hyperandrogenaemia, is a complex endocrine and metabolic disorder commonly seen in women of reproductive age. Multiple factors, including the intestinal microbiome, affect the pathogenesis and development of PCOS. However, the specific mechanisms by which gut microbes play a role in PCOS remain elusive. This review summarizes recent research about the transformational changes in gut microbes revealed in PCOS patients and the possible mechanisms and pathways by which the intestinal microbiome exerts influence on PCOS progression and phenotypes. In addition to the intestinal microbiome, evidence from animal studies suggests changes in the vaginal microbiome under PCOS conditions. The alteration of microbiome could affect oestrus cycle and PCOS phenotypes. Microbiome is closely associated with medicine and therapeutic approaches. Microbiome influences drug and therapy response and itself is a new source of therapy. Accurate modulation of the intestinal and vaginal microbiome is a potential therapy for PCOS patients. Future studies are required to elucidate the specific role of each particular genera of microbiota and the mechanism by which microbiome impacts the pathogenesis, progression and phenotypes of PCOS.