Flavonoids are important secondary metabolites, whose content and composition such as anthocyanin and flavonol have been associated with fruit quality and affect fruit coloration. Crabapple (Malus spp.), with rich color and nutritive value, belongs to the Malus genus, Rosaceae family, and it is widely used in landscape for its rich flavonoid compositions. Radiation mutagenesis breeding may increase the gene mutation frequency and enhance diversity of species, so it is a predominant approach for plant germplasm innovation. However, the changes of crabapple morphological characteristics and flavonoid compositions by radiation are not clear. In this study, we employed 60 Coγ radiation to Malus cv. 'Royalty' crabapple, and then surveyed the changes of leaves and flowers in the growth and morphology traits, color parameters, flavonoid composition, and the genetic diversity. The result found that 60 Coγ radiation decreased plant height, stem diameter and leaf and flower areas. And it promoted the flavonoids accumulation in leaves, but inhibited that in flowers. Additionally, 60 Coγ radiation improved DNA diversity. W60-7, W40-2 and W40-5 plants showed clear phenotypic variation by AFLP analysis. These results provide evidence that mutagenesis breeding may change the morphological features and flavonoid compositions, and expand crabapple germplasm resources and improve its application value.