The invention discloses a method for improving the generic cross affinity of Changbai flying ducks. The method includes the steps of first, phenotypic selection of breeding drakes; second, selection of the fecundity characters of the breeding drakes; thirdly, measurement of the affinity; and fourthly, recurrent selection measurement of the affinity. The method has the beneficial effects that the method can effectively boost the development of the duck fatty liver industry, production efficiency is improved and feeding cost is reduced; better services for human production can be achieved; the feeding cost of the breeding ducks can be reduced by 7% or above, and the duck fatty liver quality can be effectively improved; and meanwhile, the method can provide beneficial reference for breeding work of other semi-muscovy ducks of the same species, the breeding efficiency of the semi-muscovy ducks can be effectively improved and the method has great significance.