When and how the extraordinary species diversity in subtropical East Asia formed is intensely debated, and the available evidence is often inconsistent. In this study, we evaluate the effects of pre- and post- Quaternary events on the evolutionary and biogeographic history of Chinese beech (Fagus species that now occur in China) to gain new insights into the historical establishment and future fate of the East Asian subtropical forest (EASF). A series of approaches and datasets were used to reconstruct biogeographic and evolutionary history of the Chinese beech. They include phylogeography based on the polymorphisms of the complete chloroplast genomes, species distribution models, and a large palaeobiogeographic dataset including 59 pre-Quaternary fossil records, 296 Quaternary fossil records and 3515 modern pollen records. Our multidisciplinary approach suggests that (i) Chinese beech has dispersed to subtropical East Asia and diversified in the early Miocene when the Asian monsoon (AM) intensified; (ii) the last post-glacial warming resulted in limited poleward displacement but significant contraction at southern and lower elevations; (iii) the poleward dispersal of Chinese beech was limited by drought in the early growing season in temperate China, controlled by the East Asian summer monsoon. Our results support the hypothesis that the establishment of the EASF is closely related to the evolution of the AM. More importantly, we suggest that with continued climate warming (e.g., during the last post-glacial period or under current climate change), the monsoon probably hindered rather than promoted the persistence of deciduous beech species, resulting in a decline in species richness. •Phylogeography, paleobiogeography and species distribution modelling were integrated.•Asian monsoon (AM) promoted Miocene diversification of East Asian subtropical species.•AM hindered species poleward shift during the post-glacial warming period.•Hygrophilous deciduous species susceptible to mountaintop extinction.