Inherited mtDNA diseases transmit maternally and cause severe phenotypes. Currently, there is no effective therapy or genetic screens for these diseases; however, nuclear genome transfer between patients’ and healthy eggs to replace mutant mtDNAs holds promises. Considering that a polar body contains few mitochondria and shares the same genomic material as an oocyte, we perform polar body transfer to prevent the transmission of mtDNA variants. We compare the effects of different types of germline genome transfer, including spindle-chromosome transfer, pronuclear transfer, and first and second polar body transfer, in mice. Reconstructed embryos support normal fertilization and produce live offspring. Importantly, genetic analysis confirms that the F1 generation from polar body transfer possesses minimal donor mtDNA carryover compared to the F1 generation from other procedures. Moreover, the mtDNA genotype remains stable in F2 progeny after polar body transfer. Our preclinical model demonstrates polar body transfer has great potential to prevent inherited mtDNA diseases. Display omitted •PB includes few mtDNA copies due to oocyte-biased mitochondrial inheritance•PB genome transfer efficiently replaces mtDNA genotype and produces live offspring•PB1 genome transfer yields undetectable carryover of donor mtDNA in two generations•MR including PB, pronuclear, and spindle transfer do not compromise development Polar body genome transfer can effectively prevent the transmission of defective mitochondria DNA across generations, indicating the potential of this procedure to treat inherited mitochondrial diseases.