The Qinghai-Tibetan Plateau (QTP) harbors abundant and diverse plant life owing to its high habitat heterogeneity. However, the distribution pattern of biodiversity hotspots and their conservation status remain unclear. Based on 148,283 high-resolution occurrence coordinates of 13,450 seed plants, we identified hotspots by integrating data from species richness, species complementarity and spatial phylogenetics. Nine hotspot areas were identified that contained 89% of species but covered only 7% of the total land area of the QTP. Four of nine hotspots were identified firstly, including west Nyainqentanglha Mountains, the middle reaches of Lancang and Jinsha Rivers, the upper reaches of Yellow River and Qilian Mountains. Analysis of conservation efficiency indicated national nature reserves (NNRs) covered 55% of the hotspots, whereas NNRs and provincial nature reserves (PNRs) together protected 73% of the hotspots. Conservation efforts, such as establishing new protected areas and upgrading the level of existing nature reserves, should be strengthened in the conservation gaps. Targeted conservation should be carried out for species endemic to QTP due to their narrow distribution range and low conservation effectiveness. Niche modeling for 336 threatened plants indicated there were apparent range shifts of suitable habitat areas from the eastern edge to the center of the plateau under future climate scenarios, and conservation priority should be focused on the southern QTP for where have stable habitats.