[Objective] To compare the structural characteristics of intestinal flora between patients with polycystic ovary syndrome and healthy controls, and to explore the relationship between differential flora and biochemical immune indicators in patients with polycystic ovary syndrome. [Methods] From March 2018 to May 2019, 23 patients with polycystic ovary syndrome and 23 healthy women who were treated at the gynecological clinic of The Second Affiliated Hospital of Guangzhou University of Chinese Medicine were selected. Each patient retained a stool specimen and a blood specimen at the initial diagnosis. Fecal specimens were extracted from DNA for metagenomic sequencing, and serum was used to detect sex hormones and inflammatory factors. Biological information analysis was used to compare the structural characteristics of intestinal flora between patients with polycystic ovary syndrome and healthy controls. [Results] The intestinal flora of patients with polycystic ovary syndrome and healthy controls were significantly different at the Phylum, Genus and Species levels. There are 4 species with a marked difference between the two groups. The relative abundance of Bacteroides vulgatus and Escherichia fergusonii in the polycystic ovary syndrome group is higher than that in the control group, and these two bacteria are closely related to the pathogenesis of polycystic ovary syndrome. While the relative abundance of Eubacterium ventriosum and Subdoligranulum unclassified is significantly lower than that of the healthy control group. Among them, Bacteroides vulgatus, Eubacterium ventriosum and Subdoligranulum unclassified are correlated with each other, and there are correlations between different species and biochemical immune indexes. It was found that the combined of five species of Ruminococcus bromii, Gordonibacter pamelaeae, Desulfovibrio piger, Eubacterium ventriosum, Prevotella stercorea had good efficacy in the early diagnosis of polycystic ovary syndrome patients. Genetic analysis found that PWY 7228 super-pathway of guanosine nucleotides de novo biosynthesis I gene pathway is enriched in the polycystic ovary syndrome population. [Conclusion] The intestinal flora and biochemical immune parameters of patients with polycystic ovary syndrome are significantly different from those of the control group, and have a certain correlation, which provides a direction for the comprehensive diagnosis and treatment of patients with polycystic ovary syndrome.