This study aimed to assess frozen-thawed embryo transfer (FET) outcomes in natural, hormone replacement treatment (HRT) and semi-HRT cycles. This was a retrospective cohort study of 5414 cycles of patients in an academic hospital. Patients were grouped as 2216 natural cycles, 1180 semi-HRT cycles, and 2018 HRT cycles. Primary outcome measures were implantation rate, clinical pregnancy rate and live birth rate. Other parameters, such as peak endometria-thickness, were also analyzed. Patients undergoing FET with HRT obtained higher implantation rate and clinical pregnancy rate than patients with natural or semi-HR cycles (29.3% vs. 21.5% vs. 25.6%, P=0.01, and 48.7% vs. 42.7% vs. 36.1%, P=0.01, respectively). This finding was not changed in patients with thin endometrium (<= 8 mm). A Subanalysis in patients with HRT showed that the implantation and clinical pregnancy rate was higher in patients without ovulation than ovulatory patients (29.8% vs. 16.9%, P<0.01, and 49.5% vs. 26.3%, P<0.01, respectively). This study suggests that HRT increases the possibility of pregnancy. Further, our data showed that ovulation in HRT cycle has a detrimental effect on pregnancy. Therefore, we recommend that HRT should be used in FET cycles, and ovulation of patients should be evaluated during the treatment.