A breeding method for solving a color difference problem of colored fresh-eating corn grains is characterized in that conventional colchicine or herbicide induction and other chemical induction methods are adopted, a female gamete chromosomal of an amphiphilic selfing line is induced for doubling to make genotypes including a genotype controlling grain colors highly homozygous; followed by, according to color standards of varieties, grain color and depth phenotypes are subjected to genotype identification and selection; an amphiphilic selfing line with pure and uniform colors and consistent genotypes and phenotypes is obtained, finally, pure colors and uniform color depth of hybrid grains in a fresh-eating period and a hybrid mature period are achieved, and the color ratio is consistent to a theoretical value; and the breeding method has the technical effects that the color genotypes are highly homozygous, the grain colors in the fresh-eating period are pure and uniform, and the color phenotype ratio is consistent to the theoretical value. No matter compared with conventional techniques or molecular techniques, the method has the advantages of good color effect, accurate breeding result, high breeding efficiency, fast homozygous speed, low economic cost, simple techniques, easy operation, and convenience for application.