The invention discloses a method for breeding a color wheat variety and belongs to the technical field of special wheat breeding. According to the method, a white-grain wheat variety with high yield and high quality is selected to serve as a recurrent parent and hybridized with black-grain wheat, purple-grain wheat and green-grain wheat, progeny and the recurrent parent are subjected to multi-generation backcross, a wheat near-isogenic line is bred and mixed with the white-grain wheat recurrent parent in certain ratio, and a color wheat production variety is generated, wherein for the wheat near-isogenic line, plant and leaf types, agronomic characters and yield traits of the wheat near-isogenic line are close to those of the recurrent parent, and the wheat near-isogenic line has characters of the black grains, purple grains and green grains. After the color wheat variety is planted, the plant and leaf types and the agronomic characters are neat and the same, the yield is high, and harvested wheat contains white-grain wheat, black-grain wheat, purple-grain wheat and green-grain wheat, integrates color, aroma, taste and nutrition efficacy and has very good nutrition and health care functions.