The invention discloses a breeding method of radish with purple peel. According to the method, a male sterile plant of a 'dahongpao' radish is used as a sterile source, a six-generation selfing line c152b of a 'cuanxinhong' radish is used as a transformation material, and a male sterile line c152a is obtained by six-generation backcross. A 'baiyuchun' radish is used as an original material, and a high-generation selfing line s-4-3-2-5-1-6-3 with stable inheritable characters can be obtained by seven-generation single plant selfing. The male sterile line c152a is used as a female parent, and the high-generation selfing line s-4-3-2-5-1-6-3 of 'baiyuchun' is used as a male parent, so that one-generation hybrid variety, named as 'ziyu', of the radish with the purple peel can be obtained by hybrid of the male parent and the female parent. According to the obtained variety 'ziyu', the upper half part of the surface peel of a radish is light purple, the lower half part of the surface peel of the radish is white and white like the color of meat, the root peel of the radish is smooth, the peel of the radish is thin, the radish meat is relatively crisp, the content of water in the radish is relatively high, the radish has the flavors of a white radish and a red radish, the yield is high, and the radish with the purple peel can be suitable for cultivation in autumn and cultivation overwintering or in early spring in greenhouses in the middle and lower reach areas of Yangtze river.