Many biological conservationists take actions to conserve plant species with extremely small populations (PSESP) in China; however, there have been few studies on the spatial distribution of threats to PSESP. Hence, we selected distribution data of PSESP and made a map of the spatial distribution of threats to PSESP in China. First, we used the weight assignment method to evaluate the threat risk to PSESP at both country and county scales. Second, we used a geographic information system to map the spatial distribution of threats to PSESP, and explored the threat factors based on linear regression analysis. Finally, we suggested some effective conservation options. We found that the PSESP with high values of protection, such as the plants with high scientific research values and ornamental plants, were threatened by over-exploitation and utilization, habitat fragmentation, and a small sized wild population in broad-leaved forests and bush fallows. We also identified some risk hotspots for PSESP in China. Regions with low elevation should be given priority for ex- and in-situ conservation. Moreover, climate change should be considered for conservation of PSESP. To avoid intensive over-exploitation or utilization and habitat fragmentation, in-situ conservation should be practiced in regions with high temperatures and low temperature seasonality, particularly in the high risk hotspots for PSESP that we proposed. Ex-situ conservation should be applied in these same regions, and over-exploitation and utilization of natural resources should be prevented. It is our goal to apply the concept of PSESP to the global scale in the future.