The Hengduan Mountains (HDM) harbor the richest temperate diversity in the Northern Hemisphere, yet our understanding of how this exceptionally diverse biota evolved remains obscure. Large-scale historical biogeographic analyses of 851 terrestrial vertebrate species and their relatives (totaling 4862 species) reveal that multiple evolutionary pathways formed this biodiversity hotspot. Whereas in situ speciation dominates in amphibians and non-avian reptiles, near-equal in situ speciation and colonization occurs in mammals, and colonization happens primarily in birds. HDM are a 'cradle' for neo-endemics and a 'sink' receiving surrounding biotas, mostly (>30%) coming from the Indo-Malay region. Orogenesis and monsoon intensification triggered in situ speciation initiated in the early Oligocene and peaking around 7-8 Ma. Analyses of different taxonomic groups reveal contrasting evolutionary processes and how major geo-climatic events override taxon-specific attributes. Results highlight the need to incorporate taxon-specific traits into future conservation planning to effectively address the unique needs and challenges of different groups.