〔Abstract〕 Objective To explore the application of preimplantation genetic haplotyping based on next generation sequencing in process of preimplantation genetic diagnosis of monogenetic diseases. Methods The whole genome of the biopsied trophoblast cells from blastocysts was amplified by multiple displacement amplification method. The pathogenic gene mutation was selected as the target region, and some SNPs were selected as the genetic markers in the upstream and downstream of the target mutation. Preimplantation genetic haplotyping and aneuploidy screening were carried out for embryos by next generation sequencing. The results were confirmed by Sanger sequencing. Results A total of 421 oocytes were obtained from 22 patients, 355 oocytes matured, 305 oocytes fertilized, 301 oocytes cleaved and 143 blastocysts were biopsied. After haplotype analysis, 40 embryos were transplantable, there were 17 transplantation cycles, which lead to 12 clinical pregnancies and 9 live births(1 patient gave birth to 2 infants, which were monozygotic twins). All the infants were followed up in good health. The pregnancy rate was 70.6%. All haplotype analysis results were confirmed by Sanger sequencing and the results were consistent. Conclusion The preimplantation genetic haplotyping method based on the next generation sequencing is feasible, which can help families with high genetic risk to obtain healthy offspring, so as to achieve the goal of eugenics.