To elucidate the relationship among gut microbiota, metabolites, and PCOS clinical features, we characterized gut microbiota from a large number of PCOS patients with high BMI (BMI ≥ 24) and normal BMI (BMI < 24) using 16S rRNA gene sequencing and untargeted metabolomics, and their association with FKBP5 CpG methylation was also investigated. This evidence concerns the gene FKBP5 and polycystic ovary syndrome.