Gamma (γ)-irradiation can induce changes in plant morphology, cellular physiological activities, and genetic material. To date, there has been limited research on the molecular basis of leaf morphological abnormalities and physiological changes in irradiated rose plants. In this study, Rosa multiflora ‘Libellula’ plants were treated with ⁶⁰Co γ-rays. The irradiation resulted in the distortion of blade morphology. Additionally, the leaf chlorophyll content decreased, whereas the accumulation of reactive oxygen species increased. The differentially expressed genes between the control and 2–3 plants irradiated with 50 Gy were analyzed by RNA-seq technology, which revealed genes related to chlorophyll metabolism were differentially expressed. The expression levels of genes related to the regulation of antioxidant enzyme synthesis were downregulated. An RNA-seq analysis also identified the differentially expressed regulatory genes involved in leaf morphology development. Four genes (RcYABBY1, RcARF18, RcARF9, and RcWOX8) were selected, and their expression patterns in different leaf development stages and in various plant organs were analyzed. Furthermore, virus-induced gene silencing technology was used to verify that RcYABBY1 is involved in the morphogenesis of R. multiflora ‘Libellula’ leaves. The results of this study are useful for clarifying the molecular, physiological, and morphological changes in irradiated rose plants.