Objective To investigate the differences in intestinal flora characteristics between infertile patients with polycystic ovary syndrome (PCOS) and tubal obstruction and healthy women of childbearing age. Methods A total of 30 female infertile patients, who met the inclusion criteria in Reproductive Medicine Center, The First Hospital of Lanzhou University from Sep. to Dec. 2020, were enrolled and divided into PCOS infertility group (n＝20) and tubal obstruction infertility group (n＝10). Healthy women of childbearing age who underwent prenatal testing in the same hospital during the same period were recruited as healthy control group (n＝10). Fecal and blood samples were collected from each group of the participants, the characteristics of intestinal flora were detected by 16S rRNA gene sequencing, and their relationship with clinical parameters was analyzed. Results The relative abundance of Firmicutes in the PCOS infertility group and tubal obstruction infertility group were significantly decreased compared with the healthy control group at phylum level (both P＜0.05), while the relative abundances of Bacteroidota and Proteobacteria were significantly increased in the PCOS infertility group (both P＜0.05). Compared with the tubal obstruction infertility group, the relative abundance of Firmicutes was decreased and that of Proteobacteria was increased in the PCOS infertility group (both P＜0.05). Firmicutes and follicle-stimulating hormone (FSH), Bacteroidota, Proteobacteria, Actinobacteriota and total cholesterol (TC), and Actinobacteriota and homeostasis model assessment of insulin resistance (HOMA-IR) were all positively correlated in the PCOS infertility group (all P＜0.05), while Firmicutes and TC, Desulfobacterota and fasting blood glucose (FBG), and Fusobacteriota and HOMA-IR were negatively correlated (all P＜0.05). In the tubal obstruction infertility group, Campilobacterota and luteinizing hormone/FSH ratio, unidentified bacteria and triglyceride, and Firmicutes and estradiol were positively correlated (all P＜0.05), while Campilobacterota and HOMA-IR, and unidentified bacteria and waist-hip-ratio were all negatively correlated (all P＜0.05). Conclusion The composition of intestinal flora in infertility patients with PCOS and tubal obstruction is disordered and related to glucose and lipid metabolism.