Understanding the variability of extinction risk and its potential drivers across different spatial extents is crucial to revealing the underlying processes of biodiversity loss and sustainability. However, in countries with high climatic and topographic heterogeneity, studies on extinction risk are often challenged by complexities associated with extent effects. Here, using 2.02 million fine-grained distribution records and a phylogeny including 27,185 species, we find that the extinction risk of flowering plants in China is spatially concentrated in southwestern China. Our analyses suggest that spatial extinction risks of flowering plants in China may be caused by multiple drivers and are extent dependent. Vegetation structure based on proportion of growth forms is likely the dominant extinction driver at the national extent, followed by climatic and evolutionary drivers. Finer extent analyses indicate that the potential dominant extinction drivers vary across zones and vegetation regions. Despite regional heterogeneity, we detect a geographical continuity potential in extinction drivers, with variation in West China dominated by vegetation structure, South China by climate, and North China by evolution. Our findings highlight that identification of potential extent-dependent drivers of extinction risk is crucial for targeted conservation practice in countries like China.