Background: Women with polycystic ovary syndrome (PCOS) have been reported with low pregnancy rate and high OHSS risk in in vitro fertilization (IVF) programs due to the decreased endometrial receptivity and high ovarian reserve. The aim of the study was to compare the effectiveness, safety and economic cost of GnRH antagonist (GnRH-ant) and modified prolonged GnRH agonist (mGnRH-a) protocol in PCOS patients.Methods: This study was a retrospective cohort study that included 2164 women with (PCOS) undergoing assisted reproductive technology (ART) treatment from January 2014 to April 2019. Among them, 2018 women received mGnRH-a treatment and 146 women received GnRH antagonist (GnRH-ant) treatment. The two groups were matched by propensity scores with a ratio of 1:4 (GnRH-ant versus mGnRH-a) accounting for potential confounding factors. The primary outcomes were the live birth rate (LBR), incidence of moderate-to-severe OHSS and the cost of controlled ovarian hyperstimulation (COH). LBR was defined as live birth per started treatment cycle after first fresh or frozen embryo transfer.Results: Women with the mGnRH-a protocol had an increased endometrial thickness on HCG injection day, compared with GnRH-ant protocol (10.84 vs. 9.62, P<0.001), furthermore, the number of transferable embryos on day 3 (7 vs. 5, P=0.022), clinical pregnancy rate (67.81% vs. 52.74%, P=0.0007), implantation rate (56.05%, vs. 43.44%, P<0.001) and live birth rate (58.22% vs. 41.78%, P=0.0004) were also significantly higher in the mGnRH-a protocol group. However, there were no significant differences in the incidence of moderate-to-severe OHSS (4.28% vs. 2.05%, P=0.333), the incidence of severe OHSS (0.17% vs. 0%, P=1) and the cost of COH (RMB: 7736.9 vs. 8046.54, P=0.113). Conclusion: The mGnRH-a protocol has a higher live birth rate than GnRH-ant protocol with the similar safety and economic cost among infertile women with PCOS.