Subtropical China has drawn considerable attention for biogeography studies because of its high plant species diversity, which has been closely related to geo-climate changes since the Miocene. Phylogeography has become the main method for studying the influence of geo-climate changes on the distribution and genetic structure of plants. In this paper, we review the response patterns to geo-climatic changes since the Miocene and the historical causes of population-level genetic differentiation of broad-leaved forest plants in this region. During the Miocene and Pliocene, broad-leaved forest plants were forced to contract southward and form different lineages because of global cooling, the Qinghai-Tibet Plateau uplift, and Asian interior aridity. Meanwhile, the escalation of Asian monsoons provided suitable environment for diversification. During the glacial and interglacial ages in the Pleistocene, both deciduous and evergreen broad-leaved forests plants mainly underwent long-term isolation in multiple separated refugia. Different refugia populations respectively experienced localized contractions and expansions. Long-term isolation caused further divergence of different lineages, resulting in high genetic diversity and high differentiation. Few plants experienced southward contraction in glacial ages and obvious northward expansion in the interglacial ages. Finally, we speculate on the directions of future research based on accurate divergence time estimations and on mechanisms underlying the genetic structure.