<p>Protecting critical habitats globally is essential to buffer threatened species from extinction due to anthropogenic stressors. However, a limited understanding of the global distribution patterns of habitats for threatened terrestrial vertebrates and their associated habitat hotspots hinders efforts aimed at assessing biodiversity vulnerability and developing targeted conservation strategies. In this study, we integrated spatial data from the International Union for Conservation of Nature’s Red List of Threatened Species with a deep learning approach to evaluate the habitat distribution for 4,851 threatened species and construct a global niche interaction network. These habitat hotspots cover only 4% of the terrestrial surface but encompass 67.9% of all analysed species. While vast unoccupied habitats exist, 76.8% of them remain geographically isolated by continental or oceanic barriers and are significantly affected by human pressures. Species at higher risk of extinction often have a larger proportion of unoccupied habitats, but geographic isolation limits these ecological opportunities. We identified regions where unoccupied habitats are concentrated and have long-term persistence potential. Furthermore, the continued loss of native habitats for species inhabiting islands or continental margins due to human pressures may accelerate the widespread homogenization of global niches, underscoring the rarity and irreplaceability of these fragile habitats. Our global assessment provides useful perspectives on sustainable conservation planning.</p>