The invention relates to a breeding method of five-color rice. According to the breeding method, indica type white rice variety type A or Deyou 17 is used as female parents, stem type colorful rice variety Lijiang small millet is used as male parents, artificial castration pollination and hybridization is carried out, according to the seedling target, pedigree method breeding and color mode RBG (red, blue and green) selection are combined, indica and stem subspecies colorful rice with the basically identical agronomic characters including the strain height, the growth period and the like and different rice seed coat colors are obtained through seven-year and six-generation breeding, and the coarse rice colors of the five-color rice are respectively the black, the sepia, the red, the yellow and the white. The same-field planting of the rice with five colors is realized, the labor and the time are saved, the planting cost is identical to that of the conventional rice, and the yield is higher than that of other colorful rice. The five-color rice is used as the special rice, the nutrition value of the five-color rice is much higher than the ordinary rice, the market value is higher than that of the ordinary rice, and better industrial development prospects are realized.