Radiation mutation breeding is an effective method to create new Chrysanthemum morifolium germplasm, which can provide important resources for mining functional genes of ornamental plants. This review summarized the basic principles of radiation mutation breeding and the research progress of germplasm innovation and variation mechanism of radiation mutation in C. morifolium. The phenotypic variations of C. morifolium, such as flower color, flowering period, resistance, leaf shape, etc., induced by different types of ionizing radiations were illustrated. In addition, the application of high-energy heavy ion beams in germplasm innovation and the new variety breeding of C. morifolium were introduced emphatically. Meanwhile, some problems existing in radiation mutation breeding of C. morifolium were discussed, and some suggestions were given.