Observational retrospective data suggest that an artificial cycle frozen embryo transfer may be associated with a higher risk of hypertensive disorder of pregnancy than a natural cycle frozen embryo transfer among women with regular ovulatory cycles. The corpus luteum, which is not present in the artificial frozen cycles, is at least partly responsible for this poor obstetrical outcome. However, an artificial cycle is the most frequently used regimen for women with polycystic ovary syndrome undergoing frozen embryo transfer. Whether the risk of hypertensive disorder of pregnancy could be mitigated by employing physiological frozen embryo transfer protocols that lead to the development of a corpus luteum in patients with polycystic ovary syndrome remains unknown. This study aimed to investigate the impact of letrozole use during frozen embryo transfer cycles on obstetrical and perinatal outcomes of singleton and twin pregnancies compared with artificial frozen cycles among women with polycystic ovary syndrome. This retrospective cohort study involved women with polycystic ovary syndrome who had undergone artificial frozen cycles or letrozole-stimulated frozen cycles during the period from 2010 to 2018 at a tertiary care center. The primary outcome was the incidence of hypertensive disorder of pregnancy. A multivariable logistic regression analysis was performed to control for the relevant confounders. A total of 2427 women with polycystic ovary syndrome were included in the final analysis. Of these women, 1168 underwent artificial cycles and 1259 underwent letrozole treatment, of which 25% of women treated with letrozole alone and 75% of women receiving letrozole combined with gonadotropins. After controlling for maternal characteristics and treatment variables, no significant difference was noticed regarding gestational diabetes mellitus, abnormal placentation, and preterm premature rupture of membranes between groups in both singleton and twin pregnancies. For birth outcomes, the prevalence rates of preterm birth, perinatal death, and birthweight outcomes were all comparable between groups in both singletons and twins. However, singleton pregnancies resulting from letrozole-stimulated cycles had a lower risk of hypertensive disorder of pregnancy than those conceived by artificial cycles (adjusted odds ratio, 0.63; 95% confidence interval, 0.40-0.98). Furthermore, a decreased risk of hypertensive disorder of pregnancy was seen among women with twin deliveries resulting from letrozole-stimulated cycles vs artificial cycles (adjusted odds ratio, 0.52; 95% confidence interval, 0.30-0.87). In addition, the cesarean delivery rate was significantly lower for singletons but not for twins in the letrozole group compared with pregnancies from the artificial cycle group (adjusted odds ratio, 0.63; 95% confidence interval, 0.50-0.78, and adjusted odds ratio, 1.20; 95% confidence interval, 0.65-2.23, respectively). In women with polycystic ovary syndrome undergoing frozen embryo transfer, letrozole use for endometrial preparation was associated with a lower risk of hypertensive disorder of pregnancy than artificial cycles for endometrial preparation. Our findings provided a foundation that the increased risk of hypertensive disorder of pregnancy associated with frozen embryo transfer might be mitigated by utilizing physiological endometrial preparation protocols that lead to the development of a corpus luteum, such as a mild ovarian stimulation cycle for oligo- or anovulatory women.