To investigate the correlations of inflammatory factors, interleukin-6 (IL-6), IL-10, IL-13 and tumor necrosis factor-α (TNF-α), and composition of bacterial flora in the peritoneal fluid with infertility in endometriosis patients. A total of 55 patients diagnosed with endometriosis and infertility in the Gynecology Clinic of our hospital from June 2014 to July 2017 were selected as observation group, and another 30 non-endometriosis and non-infertility patients were enrolled as control group. The peritoneal fluid was extracted from patients in both groups, and the total white cell count and the percentage of leukocyte subset were determined. The total genome deoxyribonucleic acid (DNA) of microorganisms in peritoneal fluid was extracted, and the composition of microorganisms was analyzed using the Ion Torrent PGM platform (BGI). The levels of IL-6, IL-10, IL-13, and TNF-α in peritoneal fluid were detected via enzyme-linked immunosorbent assay (ELISA). Moreover, the correlations of inflammatory factors in the peritoneal fluid with endometriosis complicated with infertility were analyzed via Logistic regression analysis. The total white cell count, monocytes, neutrophils, eosinophils and basophils in endometriosis patients complicated with infertility were significantly higher than those in control group (p<0.05). Results of ELISA showed that the levels of IL-6, IL-10, IL-13, and TNF-α in peritoneal fluid of endometriosis patients complicated with infertility were significantly higher than those in control group (p<0.05). In peritoneal fluid of patients in both groups, Proteobacteria and Firmicutes were mainly dominated, followed by Actinobacillus, Bacteroidetes, Fusobacteria and Tenericutes, and there was no significant difference in the Eumycota between the two groups (p>0.05). Logistic regression analysis results showed that there were significant correlations of inflammatory factors (IL-6, IL-10, IL-13, and TNF-α) with endometriosis complicated with infertility. There are many kinds of Eumycota in the peritoneal fluid of endometriosis patients complicated with infertility, but they are not the main pathogenic factors. Inflammatory factors (IL-6, IL-10, IL-13, and TNF-α) can be used as important reference indexes for the diagnosis of endometriosis complicated with infertility.