A large proportion of Earth’s plant species diversity is threatened with extinction. Unprecedented anthropogenic activities are the main drivers, with habitat loss due to land transformation and unsustainable use being the most important factors. These anthropogenic activities are not just a contemporary phenomenon, but also have a long history, and their historical dynamics may shape distributions of threatened plants. However, the relative roles of historical and current changes in anthropogenic activities in determining the distribution of threatened plant species across large geographic regions have hitherto been rarely studied. In this study, for the first time, we linked the distribution of threatened species across China to current and historical changes in human population densities, cropland area, and pasture area since 1700 (at a 100 km × 100 km resolution). We find that variables describing historical changes in human impacts were consistently more strongly associated with proportions of threatened plants than variables describing current changes in human impacts. Notably, threatened plant species in China tend to be concentrated where historical anthropogenic impacts were relatively small, but anthropogenic activities have intensified relatively strongly since 1700. Hence, threatened species are likely to be concentrated in areas that have only recently come under anthropogenic pressure.