Objective To explore the impact of gonadotropin-releasing hormone agonist (GnRH-a) super-long protocol on embryo implantation rate and clinical pregnancy rate of in vitro fertilization and embryo transfer (IVF-ET) in patients with moderate-to-severe endometriosis. Methods This retrospective study included 120 women with endometriosis who received IVF-ET from Jun. 2012 to Jul. 2016 in Reproductive Medical Center of Changhai Hospital of Second Military Medical University. Among the 120 patients, 42 received super-long GnRH-a protocol, 38 received long GnRH-a protocol, and 40 received short GnRH-a protocol during IVF-ET. We compared:(1) The patients' age, infertility years, basal serum levels of follicle stimulating hormone (FSH), luteinizing hormone (LH) and estradiol (E₂), and the levels of FSH, LH, E₂ and progesterone on the human chorionic gonadotropin hCG day; (2) the average number of retrieved oocyte, fertilization rate, cleavage rate, number of available embryos, embryo implantation rate and clinical pregnancy rate. Results (1) There was no significant difference in general characteristics between three protocols. (2) Compared with the short GnRH-a protocol group, the super-long GnRH-a protocol and long GnRH-a protocol had significantly decrease serum LH and progesterone levels on the hCG day (all P<0.05). (3) The fertilization rate, cleavage rate, embryo implantation rate and clinical pregnancy rate of super-long GnRH-a protocol were significantly higher than those of the short GnRH-a protocol (P<0.05). Conclusion The IVF-ET using super-long GnRH-a protocol can improve the embryo implantation rate and clinical pregnancy rate of the patients with moderate-to-severe endometriosis compared with using long or short GnRH-a protocol.