There are about 10% of the world’s land plants in China, of which 11% are threatened species. Here, we used China as a proxy to identify hotspots of threatened species, evaluate the effectiveness of current conservation networks and assess the correlations between distribution patterns of different groups. We built the most complete database of 3,881 species of threatened land plants in China (TLPCs) to date, based on 43,710 occurrence records at county level. A total of 467 counties identified as hotspot by species richness, complementarity, and weighted algorithms, mostly confined to the mountainous areas in southern China, which account for 15.58% of land area, however, hold 95.34% of the total TLPCs. The correlation analysis revealed weak to moderate relationship between the distribution patterns of three groups (bryophytes, ferns, and gymnosperms) and angiosperms of TLPCs. We found 86.34%, 84.05% and 95.77% of TLPCs protected by NNRs, PNRs and NRs [nature reserves, including both national NRs (NNRs) and provincial NRs (PNRs)], respectively. Besides, there were 41.11% and 18.84% of hotspots identified as conservation gaps of NNRs and NRs, respectively. In conclusion, the NNRs do not play a more dominant role in conserving TLPCs diversity in comparison to PNRs. We proposed that conservation planning need to be established in the periphery of Yunnan-Guizhou Plateau due to a large number of hotspots and conservation gaps located in this area. Since a large proportion of unprotected TLPCs are critically endangered and narrow-ranged species, it is urgent to set priorities for their conservation in the nearest future.