Tulip, being an important ornamental plant, generally requires lengthy and laborious procedures to develop new varieties using traditional breeding methods requires. But ionizing radiation potentially accelerates the breeding process of ornamental plant species. The biological effects of γ-ray irradiation on tulip, therefore, were investigated through establishing an irradiation-mediated mutation breeding protocol to accelerate its breeding process. ISSR-PCR molecular marker technique was further used to identify the mutants of phenotypic variation plants. This study showed that low irradiation doses (5 Gy) stimulated bulb germination to improve the survival rate of tulip, while high irradiation doses (20 to 100 Gy) significantly (P < 0.05) inhibited its seed germination and growth, and decreased the flowering rate, petal number, flower stem length and flower diameter. More than 40 Gy significantly (P < 0.05) decreased the total chlorophyll content and increased the malondialdehyde (MDA) content in tulips. Interestingly, three types of both stigma variations and flower pattern variations, and four types of flower colour variations were observed. With increasing the irradiation dose from 5 to 100 Gy, the anthocyanin and flavonoid contents continuously decreased. Scanning electron microscopy (SEM) analysis evidenced that high irradiation doses altered the micromorphology of leaf stomata. Microscopic observations of tulip root apical mitosis further showed the abnormal chromosomal division behaviour occurring at different mitotic phases under irradiation treatment (80 Gy). Increasing the irradiation dose from 20 to 100 Gy enhanced the micronucleus rate. Moreover, the suspected genetic variation in tulips was evaluated by inter-simple sequence repeat (ISSR) analysis, and the percentage of polymorphic bands was 68%. Finally, this study concludes that that 80 Gy may be an appropriate radiation does to better enhance the efficiency of mutagenic breeds in tulip plants. Using γ-ray irradiation, therefore, is expected to offer a theoretical basis for mutation breeding in tulips.