As being impacted by complex geological events and climate change, it is of considerable significance to study the flora and biogeography of East Asia. In this study, the phylogeny of 18 species and subspecies of Acer Sect. Palmata were reconstructed to infer the biogeographic history in East Asia, using three DNA chloroplast fragments (psbA-trnH, rpl16 and trnL-trnF). With 341 (15.2%) mutation sites and 231 (10.3%) effective information sites in a total length of 2,232 bp, these 18 taxa were highly supported as a monophyletic group. The divergence of species within Sect. Palmata was mostly concentrated in the Miocene, but even then, the diversification rate remained stable. It is speculated that the ancestral area of Sect. Palmata is on the East-Asian continent, while island species are distributed in different branches. Phylogenetic analyses showed that Southwest China is the center of origin of Sect. Palmata. The occurrence of East China Sea landbridge during the Last Glacial Maximum (LGM) affected dispersal and colonization of species in East Asia directly (e.g., A. japonicum, A. oliverianum subsp. formosanum and A. tutcheri). Multiple upward expansion of species at the same latitude were appeared in Sect. Palmata on subtropical Asian continent. This study is helpful to the further understanding of the phytogeography in East Asia.