Magnolia officinalis subsp. officinalis and M. officinalis subsp. biloba are important medicinal plants in China. The bark of these two subspecies is commonly used in the production of a widely-used Chinese traditional medicine named ‘Houpu’. In recent years, M. o. subsp. officinalis and M. o. subsp. biloba have become increasingly threatened owing to the over-harvesting of their bark and the fragmentation of their habitats. In this study, we aimed to support the conservation and cultivation of these two subspecies in China by: (1) assessing the relationship between numerous environmental variables and the geographical distributions of the subspecies; (2) analysing the environmental characteristics of suitable habitats for both subspecies and predicting the spatial distribution of these habitats in China; and (3) identifying conservation areas of both subspecies in China via overlay analysis. We also assessed the degree of human disturbance within suitable habitats. We found that temperature was a major determinant for the distribution of M. o. subsp. officinalis. Conversely, the distribution of M. o. subsp. biloba was primarily dependent on precipitation rather than temperature. Distinct habitat preferences were observed between M. o. subsp. officinalis and M. o. subsp. biloba. Suitable habitats of M. o. subsp. officinalis were primarily distributed in the northern subtropical areas of China, with greater fluctuations in ambient temperature, lower extreme temperatures, less precipitation and greater fluctuations in precipitation. Habitats suitable for M. o. subsp. biloba were highly fragmented and were distributed in the central subtropical areas of China. We found that a large proportion of suitable habitats were not in the protected areas and that they were significantly disturbed by human activity. This analysis could provide useful information for the conservation of both M. o. subsp. officinalis and M. o. subsp. biloba and could aid in the selection of cultivation sites.