Malus 'Baiyun' (registration no. 20210210), a new crabapple cultivar, was registered in 2021 by the Nanjing Forestry Unversity. However, the difficult rooting has greatly limited the production of high-quality M. 'Baiyun' in industrialization development. There is thus a pressing need to develop an organogenesis protocol for the in vitro propagation of M. 'Baiyun' to alleviate a shortage of high-quality M. 'Baiyun' seedlings. The results showed that choosing the apical bud in mid-March was an excellent explant material. To promote proliferation, the highest proliferation (6.27) of apical shoots was cultured on Murashige and Skoog (MS) medium supplemented with 0.5 mg·L-1 6-benzylaminopurine(6-BA) + 0.05 mg·L-1 indole-3-butyric acid (IBA). Subsequently, a 100% rooting rate, average number of roots per shoot of 6.2 and maximum length of roots of 4.96 cm were obtained on half-strength Murashige and Skoog (1/2 MS) medium with the application of 0.5 mg·L-1 naphthaleneacetic acid (NAA) or 0.6 mg·L-1 NAA + 0.7 mg·L-1 IBA. Additionally, thick and lateral roots were obtained with 0.6 mg·L-1 NAA + 0.7 mg·L-1 IBA. Our study is the first to establish an effective organogenesis protocol for new crabapple cultivars using stem segments.