Changes in future climate will have a great impact on biodiversity. Magnolia wilsonii, an endangered tree native to China, has important scientific and medicinal value occurring in western Sichuan, northern Yunnan and western Guizhou. And it has severely declined and become critically endangered in the last years due to habitat loss and fragmentation. In this study, we modeled the current and future distributions of M. wilsonii under three representative concentration pathways (SSP1-2.6, SSP2-4.5 and SSP5-8.5). The results showed that the AUC values of all simulations were greater than 0.940. The key environmental variables affecting the potential distribution of M. wilsonii were the annual precipitation (573-1671 mm), the min temperature of coldest month (10.1ºC-16.2ºC), the coefficient of variation in precipitation seasonality (11.5-160.9), and the standard deviation of temperature seasonality (404.7- 1765.6). The area of the highly suitable habitat was 29.66×10⁴ km², mainly concentrated in Yunnan, Sichuan, Guizhou and Guangxi. Yunnan had the largest suitable habitat, occupying 13.23×10⁴ km², accounting for 44.6% of the highly suitable area. Under the three climate change scenarios, the areas of the suitable habitat of M. wilsonii showed increasing trends, the geometric center of the highly suitable habitat would move to the northeast. Our results can provide a scientific basis for the protection, cultivation, management and sustainable use of M. wilsonii.