The invention relates to a 12C<6+> ion beam radiation type breeding method for an isatis tinctoria. The method comprises following steps of (1) selecting two kinds of parent materials according to a breeding objective, wherein one is a local germplasm with the relatively strong stress resistance, selected from local varieties, and the other is a breeding material selected from Anhui isatis tinctoria germplasm; (2) carrying out reciprocal cross on the two kinds of parent materials, then screening and reserving seeds for planting; (3) soaking the seeds in warm water, and then drying or naturally air drying, so as to obtain dried seeds; (4) soaking the dried full seeds, then air drying water on the surfaces of the seeds, irradiating a sample by a 12C<6+> ion beam, so as to obtain irradiated seeds; (5) planting the irradiated seeds in a field so as to obtain a first-generation group, carefully choosing 200 variation single plants according to the original parent; (6) continuously planting the variation single plants, harvesting, reserving seeds from second-generation single plants, continuously reserving seeds and breeding to obtain third-generations plants and fourth-generation plants; and (7) identifying and testing excellent mutation strains. The method has the high efficiency and realizes the purposes of synchronous improvement of multiple characters such as yield, quality and stress resistance within a short breeding period.