Geological and climatic changes in the Quaternary of the Qinghai–Tibet Plateau (Q-T Plateau) strongly affect the migration route and distribution pattern of the plants in this region. The Angelica nitida Wolff endemic to the Q-T Plateau was used as a model to examine the response to Quaternary climatic oscillations. Three chloroplast DNA fragments (trnD–trnT, trnQ–rps16, rpl32–trnL) were sequenced and 20 haplotypes were identified. The 20 haplotypes clustered into four major clades, which were associated with geographical distribution, and the populations from the edge of the Q-T Plateau contained 19 haplotypes. Based on the average substitution rate, the divergence time in A. nitida was estimated at 1.1 million years ago (Mya), 0.80 Mya, and 0.70 Mya, corresponding to the recently continuous uplift of the Q-T Plateau and the interglacial in the Quaternary. A significant phylogeographic structure was presented (NST > GST, P < 0.01). Our results also suggested that multiple refugia for A. nitida were located on the edge of the Q-T Plateau in the Quaternary. The restricted gene flow and past fragmentation were likely the major processes that shaped the present-day spatial distribution of haplotypes in this species. These results suggested that past fragmentation mainly resulted from the maximum glaciation advance on the Q-T Plateau. The uplift of Loess Plateau, Huya fault of Minshan Mountain could also play important roles responsible for the present phylogeographical pattern of A. nitida.