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Background Owing to the crucial role the endometrium plays in embryo implantation, the four main endometrial preparation protocols have become important factors in the study of pregnancy outcomes in the FET cycles. Previous studies have shown that the best of these four protocols remains controversial for women undergoing FET. Methods A total of 10333 FET cycles from January 2018 to December 2018 were analyzed in this study. They were categorized into four groups according to endometrial preparation regimen: natural cycles (Group NC,n = 815), hormone replacement therapy cycles (Group HRT ,n = 6434), GnRH agonist artificial cycles (Group GAC,n = 1392) and ovarian stimulation cycles (Group OC, n = 1692). All patients were followed up for at least 1 year. Pregnancy outcomes were compared between the four groups and multiple logistic regression models were used to adjust for the effects of confounding factors. Results The ectopic pregnancy rate (P = 0.627) and miscarriage rate (P = 0.164) were not statistically significant between the four groups. Moreover, biochemical pregnancy rate, clinical pregnancy rate and live birth rate in the NC group were not statistically significant compared to the other three groups. After adjusting for covariates, multiple logistic regression analysis showed no statistical significance in pregnancy outcomes in the HRT, GAC and OC groups compared to the NC group.And the adjusted OR for live births was 0.988 (95 % CI0.847-1.152) for the HRT group, 0.955 (95 % CI0.795-1.146) for the GAC group,0.898 (95 % CI0.754-1.070) for the OC group. Conclusions Our study showed that natural cycles have similar pregnancy outcomes in terms of clinical pregnancy and live birth to the other three endometrial preparation options. As it has other advantages, the natural cycle protocol can therefore be the recommended option for endometrial preparation in the FET population.