Objective To observe the outcome of frozen-thawed embryo transfer (FET) between the short-time and long-time culture embryos of the infertile patients whose endometria were prepared with natural or hormone replacement cycle protocol. Methods A total of 293 patients and 337 FET cycles were enrolled, and all cycles were divided into two groups depending on their means of preparing the endometria: natural cycle (NC) protocol (NC group) and hormone replacement cycle (HRT) proto-col (HRT group), each group was divided into two layers according to the culture time of thawed embryos in vitro: short-term and overnight layers. The outcomes of clinical pregnancy rate (CPR), implantation rate (IR), spontaneous abortion rate (SAR) and multiple pregnancy rate (MPR) per cycle were compared. Results In the NC and HRT groups, the IR was respectively 32.69%and 21.83%, the CPR was 59.15%and 41.73%, the SAR was 7.14%and 16.22%, the MPR was 21.43%and 13.51%, respectively, and the IR and CPR were all higher in the NC group than those of the HRT group (all P<0.05).In the short-term and overnight layers of the NC group, the IR was 28.13%and 35.87%, the CRP was 53.57%and 62.79%, the SAR was 6.67%and 7.41%, and the MPR was 20.00%and 22.22%, respectively; no significant differences were found between the two groups. Similarly, in the HRT group's different culture time layers, the IR was 21.92%and 21.74%, the CRP was 44.19%and 39.42%, the SAR was 21.05%and 11.11%, and the MPR was 12.28%and 14.81%, respectively; no statistically significant difference was found. In short-term layer, the outcomes of FET were not statistically different between the NC group and HRT group. Compared with the overnight layer of HRT group, IR and CPR were all higher than in the overnight layer of NC group (all P<0.05).Conclusion Endometrium prepared with NC protocol can obtain a better FET outcome than that of the HRT protocol, which mainly embodied in the selection of the thawed embryos' culture time in vitro before transplant, and culture overnight is appropriate. [ABSTRACT FROM AUTHOR]