The invention discloses a method for breeding functional formula rice varieties, belonging to the technical field of special rice breeding. The method is characterized by comprising the following steps of selecting a rice variety with larger extending area and good quality in production as the recurrent parent, crossing the recurrent parent with black rice, purple rice, red rice, glutinous rice and giant embryo rice respectively, backcrossing the offsprings with the recurrent parent, breeding the near-isogenic lines which have agronomic traits similar to the agronomic traits of the recurrent parent and respectively have the traits of the black rice, purple rice, red rice, glutinous rice and giant embryo rice and mixing the seeds in proportion to prepare the seeds for production of the formula rice. The method has the following beneficial effects that after the formula rice varieties bred by the method are planted, the shapes of plants and leaves and the agronomic traits are neat and consistent; the rice obtained by grinding unhulled rice can simultaneously contain the five functional rice, namely the black rice, the purple rice, the red rice, the glutinous rice and the giant embryo rice; the functional formula rice can be produced by planting the seeds; the production method is simple and is high in efficiency and good in benefits; and the produced high nutrition functional formula rice integrates color, aroma, taste and nutrition curative effect and has good health care function.