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Background: Endometriosis can affect the systemic metabolic indicators, including body mass index, glucose metabolism and lipid metabolism, while the association between metabolic indexes and the occurrence and ART outcome of endometriosis is unclear. We aimed to evaluate the characteristics of systemic metabolic indexes of endometriosis patients with infertility and their effects on pregnancy outcome after ART treatment. Methods:A retrospective cohort study involve 412 endometriosis patients and 1551 controls was conducted. Primary outcome was metabolic indexes, and secondary measures consisted of the influence of metabolic indexes on the number of retrieved oocytes and ART outcomes, as well as the relation between blood glucose and prevalence of GDM. Results:Endometriosis patients had higher INS [6.90(5.10-9.50) vs 6.50(4.80-8.90) μU/mL, P = 0.005]. A prediction model for endometriosis combining the number of previous pregnancies, CA125, fasting blood Glu and INS, had a sensitivity of 73.9%, specificity of 67.8% and area AUC of 0.77. There were no significant differences in ART outcomes and complications. The levels of Glu were associated with GDM both in endometriosis group (aOR 12.95, 95% CI 1.69–99.42; P = 0.014) and in control group (aOR 4.15, 95% CI 1.50–11.53; P = 0.006). Conclusions: Endometriosis patients had abnormal metabolic indexes, in which serum Glu and serum INS are related to the occurrence of endometriosis, the number of retrieved oocytes and the occurrence of GDM. A prediction model based on metabolic indexes was established, representing a promising non-invasive method to predict endometriosis patients with known pregnancy history.