To evaluate the pregnancy outcomes and the safety of neonates born following frozen-thawed cleavage embryos with blastomere loss. Multicenter prospective study including all frozen-thawed cleavage embryo transfer (FET) cycles was conducted in China. A total of 9,846 transfer cycles with only intact embryos and 2,259 transfer cycles with only blastomere-lost embryos were included. FET pregnancy outcomes including implantation rate, clinical pregnancy rate, pregnancy loss rate, pregnancy termination due to fetal defects, stillbirth and live birth rate were assessed. The outcomes of neonates born following the transfer of blastomere-lost embryos were compared to those born following the transfer of intact embryos using multilevel logistic regression. A total of 12,105 FET cycles were included in analysis (2,259 cycles in blastomere loss group and 9,846 cycles in intact embryo group). Compared with FET cycles of intact embryo, embryo with blastomere loss transfers showed significantly poorer outcomes with respect to implantation rate, pregnancy rate and live birth rate. However, following embryo implantation, the two groups were similar with respect to live birth rate per clinical pregnancy. Among the 4229 neonates, multiples neonates born from embryos with blastomere loss were at an increased risk of SGA (aOR=1.50, 95%CI, 1.00-2.25). Similar results were observed among singletons (aOR=1.84, 95%CI, 0.99-3.37), however, the confidence interval did not exclude the null effect. No association were found between blastomere loss and subsequent occurrence of congenital anomalies or neonatal mortality. However, neonates born from blastomere-lost embryos showed an increased risk of transient tachypnea of the newborn (TTN, aOR=5.21, 95%CI, 2.42-11.22). Transfer of embryos with blastomere loss was associated with a reduced rates of conception. Once embryos with blastomere loss are implanted, pregnancies appear to have the same probability of progressing to live birth, but with an increased risk of SGA and TTN.