In order to provide better guarantee on technical support for the future innovation of common buckwheat resources and new variety breeding, this study investigated the effective method of isostyle resources in innovation of common buckwheat. The positive and negative hybridization tests by using isostyle germplasm resource crossing with common buckwheat cultivars showing different flower types were carried out. Six hybridization combinations (isostyle × cultivar, isostyle × long style, isostyle × short style,cultivar × isostyle, long style × isostyle, short style × isostyle) were achieved, and they were subjected for analyzing the seed-fertility and the inheritance segregation. The results showed that the fertility rate of isostyle common buckwheat resources was observed up to 22.6%, significantly higher than that of common buckwheat. Regarding to the hybrids for selecting the new isostyle pure lines, the "long style × isostyle" hybrid pattern was the best pattern. Otherwise, the "isostyle × cultivar" was optimal for the selection of new strains. Taken together, this study suggested the feasibility on hybridization techniques in order to meet the demand of the resource innovation. The offspring plants were observed with obvious phenotypic variation, which might suggest a possibility to effectively solve the bottleneck problem in common buckwheat cross breeding.