Triosteum pinnatifidum Maxim., an alpine plant, is traditionally used for several medicinal purposes. Here, both chloroplast DNA sequences and nuclear low copy sequence markers were used to investigate the genetic diversity and population structure of T. pinnatifidum. Materials were collected from thirteen localities in the northeast Qinghai–Tibet Plateau (QTP) and adjacent highlands and advanced analytical toolkits were used to access their origin and range shifts. The results revealed a higher level of population differentiation based on chloroplast DNA (cpDNA) concatenated sequences compared with the nuclear DNA sequences (F_ST = 0.654 for cpDNA, F_ST = 0.398 for AT103), indicating that pollen flow was still extensive in T. pinnatifidum. A decline in haplotype variation was observed from the plateau edge and adjoining highlands toward the platform of the QTP. The hypothesis “dispersal into the QTP,” proposing that T. pinnatifidum experienced migration from the plateau edge and adjacent highlands to the platform, was supported. These results were in line with the hypothesis that multiple refugia exist on the plateau edge and adjacent highlands rather than on the plateau platform. Our unimodal mismatch distribution, star-like network supported a recent expansion in T. pinnatifidum.