Abstract Background Medicinal plants have always played an important role in the history of human health. However, the populations and sustainable use of medicinal plants have been severely affected by human activities and climate change. Little is known about the current conservation status and distribution pattern of medicinal plants. In this study, based on accurate geographical distribution information of 9756 medicinal plants, we identified diversity hotspots and conservation gaps, evaluated conservation effectiveness of nature reserves, and predicted suitable habitat areas for medicinal plants in China to provide scientific guidance for their long-term conservation and sustainable use. Results A total of 150 diversity hotspot grid cells, mainly concentrated in central and southern China, were identified. These only accounted for 5% of the total distribution area but contained 96% of the medicinal plants of the country. The hotspot grid cells included all traditional hotspot areas, but we also detected three new hotspots, namely Mufu-Lushan Mountains, Tianshan-Altai Mountains, and Changbai Mountains. The current national and provincial nature reserves protect 125 hotspot grid cells, which harbor 94% of all medicinal plants. However, 25 hotspot grid cells, distributed in the Tianshan-Altai Mountains and Hengduan Mountains, are located outside the national and provincial nature reserves. An analysis of the predicted effects of climate change indicated that the suitable habitat areas will shift from southern to northern China, and that southern China will face a considerable loss of suitable habitat areas, while the east and west parts of China will encompass remarkably more suitable habitat areas in the future. Conclusions The current conservation networks have achieved high conservation effectiveness with regard to medicinal plants; however, the conservation gaps we identified should not be neglected, and conservation planning needs to take into account the predicted shifts of some hotspots of medicinal plants due to climate change.