Chinese cherry (Prunus pseudocerasus) has many natural tetraploid species within Prunus. The pollen grains of tetraploid Chinese cherry are hetero-diploid, the two S-haplotypes in the pollen are a combination of two of the four possible S-haplotypes. The abnormal segregation ratios ofpollen-S indicate that a few hetero-diploid pollen grains could inactivate self-stylar S-RNase inside the pollen tube and grow better into the self-ovaries than to the others. In this study, three Chinese cherry cultivars, “Daiba” (S1S2S5S8), “Taishanganying” (S1S2S4S6), and “Laiyangduanzhi” (S1S2S8Sx), were used to investigate the inheritance of hetero-diploid pollen-S alleles in non-self receptors. Genetic analysis showed that the distribution of S-haplotypes is unequally expressed in self- and cross-pollinated progenies. The S2-haplotype, which is found with lowest frequency in all progeny plants, is a likely lethal mutation. Moreover, the number of individuals with two different S-haplotypes was also unequal in the two cross-pollinated progenies. Notably, the number of individuals with S1S5 and S1S8 genotypes was larger than other genotypes in the cross-pollinated progeny of “Laiyangduanzhi”דDaiba”, and the number of individuals withS1S4, S1S6, and S4S6 genotypes was larger than S2-haplotypes in the cross-pollinated progeny of “Laiyangduanzhi”× “Taishanganying”. These results indicate that only a few genotypes of hetero-diploid pollen grains have the capability to grow into the ovaries of “Laiyangduanzhi”. Interestingly, the pollen grains with S5S8 genotypes, which is self-compatible, was incompatible with the styles of “Laiyangduanzhi”, while the pollen grains with S1S8, S1S6 and S4S6 genotypes, which are self-incompatible, were compatible with the styles of“Laiyangduanzhi”.