OBJECTIVE: To apply single cell sequencing based on multiple annealing and looping amplification cycles (MALBAC) for the determination of the rate and type of mosaicisms of high-quality embryos at cleavage stage. METHODS: After thawing and removing of zona pellucida by enzymatic digestion, blastomeres were collected the high-quality embryos donated by couples whom had given birth to healthy offspring by intracytoplasmic sperm injection and embryo transfer. The whole genome of single cell was amplified and subjected to next generation sequencing. RESULTS: From a total of 23 embryos, 184 blastomeres were collected. 175 (95.1%) of the blastomeres were successfully sequenced, of which 100 (57.1%) were found to harbor chromosomal aneuploidies. Among the 23 embryos, 3 (13.0%) were diploid, 20 (87.0%) were mosaicisms, which included 5 (21.7%) aneuploid mosaicisms, 7 (30.4%) diploid-aneuploid mosaicisms, 5 (21.7%) abnormal mosaicisms, and 3 (13.0%) irregular segregations. CONCLUSION There is a high rate of chromosomal mosaicisms in high-quality cleavage embryos. Mosaicisms of complex chromosomal abnormality or with high proportion of abnormal cells may be an important factor affecting the potential of embryonic development.