For centuries, ecologists have been captivated by the assembly of local communities from regional species pools, which gives rise to spatial diversity patterns. This study focused on hierarchical filtering process, which involves dispersal limitation and climatic constraint across regional to local scale, that underpins plant biodiversity patterns in East Asian islands, as one of the biodiversity hotspots with high endemicity. We used vegetation and species pool datasets of angiosperm woody plant communities collected from seven mountains across Japan to Taiwan to explore the relative contributions of local factors of individual plots, islands, latitude, elevation, and climatic variables related to the pattern of phylogenetic community assembly. Using linear regression and variation partitioning, we found that the island factor had the strongest filtering effect followed by latitude. Elevation and local factors (slope, aspect) accounted for a very small proportion of the variance in phylogenetic dispersion and community clade age between member species. Geographical factors involving islands, distance, and elevation had overriding filtering effects over climatic factors (minimum temperature of the coldest month, precipitation of the driest month) in shaping woody plant assembly patterns at the regional scale across East Asia islands. Tropical niche conservatism contributed to shaping woody plant communities in temperate region and high elevational regions on subtropical mountains as young and closely related species coexisted in those regions due to their adaptation to cold climates. This also explained the minor climate effects on species sorting in temperate mountains characterized by temperate-specific species pool which had already been filtered by cold climates. Inconsistent elevational phylogenetic diversity patterns in East Asia islands suggest a mountain-specific process that governs community assembly along elevational gradients, likely attributed to the location and climate of the mountain. These results suggest that historical factors (geohistorical isolation) related to islands and mountains contribute to in situ diversification that shaped plant diversity gradient from subtropical to temperate forests.