Pedicularis longiflora experienced extensive populations' expansion in Quaternary, but the dispersal corridors were still unclear. According to the distribution patterns of haplotypes based on chloroplast DNA variation, the dispersal routes were predicted using species distribution models (MXENT) and the least-cost path method. Two possible dispersal routes from the southeastern part of Tibetan Plateau (TP) to interior were identified. The populations of East Himalayas-Hengduan Mountains region expanded to the western part of TP along with the Yarlung Zangbo River valley and the lower altitudes of the north slope of Himalayas. The expansion trend was also proved by SDMs based on two historical periods containing the Last Interglacial and the Last Glacial Maximum. In conclusion, identification of dispersal routes is significant to the evolutionary history of alpine plants and the protection of special species in TP.