Loquat [Eriobotrya japonica (E. japonica)], a small genus of the subtribe Malinae that consists of ≈30 species, is an evergreen rosaceous fruit tree that is native to southeastern China, and some wild species that possess novel, favorable traits have excellent breeding potential. For example, Eriobotrya bengalensis blooms in late spring and ripens in early autumn in Guizhou Province, China, which prevents cold injury in winter by breeding spring-flowering cultivars using the special characters. Therefore, in the present study, the pollination treatments of cut-style pollination were evaluated that may promote successful distant hybridization in Eriobotrya japonica ‘Dawuxing’ × Eriobotrya deflexa and E. japonica ‘Dawuxing’ × E. bengalensis. The results indicated that the impairment of the pollen tube growth in the upper third of the style after pollen germination is an important factor leading to the failure of distant hybridization between the species tested in E. japonica, and that cut-style pollination can effectively overcome prefertilization barriers of the distant hybridization combination. Furthermore, the results of allele-specific polymerase chain reaction (AS-PCR) showed that S-genotypes, in accordance with the S-RNase heredity to separate the rule completely in offspring, should be both parents' S-RNase, and that the random 50 seedlings of Eb-2 and Ed-2 are true hybrids.