There are currently various protocols for in vitro fertilization (IVF). For patients with polycystic ovarian syndrome (PCOS), an optimized protocol for the downregulation of pituitary follicle stimulating hormone and luteinizing hormone via gonadotropin-releasing hormone agonist (GnRHa) remains a challenge. In the present study, the primary endpoint of an ultra-long and a conventional long GnRHa protocol for intracytoplasmic sperm injection/IVF treatments of patients with PCOS was retrospectively compared. In the modified ultra-long protocol group, endometrial thickness, morphology, and blood flow were significantly improved, as compared with in the conventional long protocol group. Furthermore, the serum progestogen (P) concentrations and P/estrogen (E2) [(Px1,000/E2)] ratio on the day of human chorionic gonadotrophin administration were significantly decreased in the modified ultra-long downregulation group, whereas the pregnancy and implantation rates were significantly higher. There were no significant differences in the average number of obtained oocytes, good quality embryo rates, cancel rates, fertilization rates, abortion rates, serious ovarian hyperstimulation syndrome incidences, ectopic pregnancy rates or gonadotropin (Gn) dosages between the two groups. These results suggest that the modified ultra-long protocol plus human menopausal Gn medication may be superior to the conventional long protocol, and may lead to improved implantation and pregnancy outcomes for infertile patients with PCOS.