OBJECTIVE To compare the clinical outcomes of GnRH agonist (GnRH-a) long protocol and GnRH antagonist (GnRH-ant)protocol in vitro fertilization (IVF)-embryo transfer (ET) cycles, and to explore the optimized protocol for infertile women. METHODS From June 2010 to June 2012, 2 444 infertile women underwent their IVF cycles in Peking University Third Hospital, which were divided into 1 706 GnRH agonist long protocol and 738 GnRH antagnist protocol groups. The data of the general demographic, treatment and clinical outcome were compared between the two groups. RESULTS The age, body mass index(BMI), infertile duration, antral follicle count (AFC) did not reach statistical difference, the level of estradiol on the day of HCG: injection was higher in GnRH agonist group [(10 595±7 368)pmol/L vs. (9 087±7 035) pmol/L], and the mean length of stimulation was longer in GnRH agonist group[(12.5±1.8) d vs.(9.4±1.7) d], The dose of Gn [(3 107±1 377) IU vs. (2 084±903)IU]was higher in GnRH agonist group. The number of ovum was 13.4±6.6 in GnRH agonist group and 11.8±6.4 in GnRH antagonist group. Those clinical parameters all reached statistical difference (P<0.05). The number of the transfer embryos, fertilization rate, and cleavage rate did not reach statistical difference, but the number of the embryos was 5.6±4.5 in GnRH agonist group and 5.1±4.3 in GnRH antagonist group,reached statistical difference (P<0.05). The abortion rate, embryonic death rate, ectopic pregnancy rate, preterm labor rate, postterm pregnancy rate, fatal malformations rate showed no statistical difference, but the GnRH agonist long protocol had higher pregnancy rate (44.0% vs. 38.3%), and higher term pregnancy rate (64.2% vs. 56.9%) compared with GnRH antagonist protocol, thus those parameter reached significant difference (P<0.05). CONCLUSION Compared with GnRH-antagnist protocol, GnRH agonist long protocol had higher pregnancy rate and better pregnancy outcome.