We studied 1616 bp of mtDNA sequence in plateau pika Ochotona curzoniae sampled from 10 geographical regional groups to study the population history as well as long-term gene flow of O. curzoniae. We detected 153 haplotypes in 245 individuals. Mismatch analyses detected rapid population expansion in nine regional groups. Long-term estimates of gene flow revealed a unidirectional manner from peripheral groups towards central plateau groups. In contrast, gene flow among central plateau groups was bidirectional. Our results indicate that the population expansion of most groups occurred 0.24–0.03 Mya, which mostly coincides with the interglacial period before the last glacial maximum. Gene flow of O. curzoniae was closely related to the different effects of the extensive glacial period (EGP) and the last glacial period (LGP) on the species. The EGP had caused extinction of all central populations, while the LGP had very limited influence on the populations that recolonized the central region. However, the glaciers in the relatively humid areas surrounding the interior of the plateau during the LGP were substantial and had prevented or greatly reduced the ‘counter’ gene flow from the central populations to the edge populations, resulting in a unidirectional gene flow. A hierarchical analysis of molecular variance showed that 55.1% of the total variance was explained by among-groups structuring while 34.2% was explained by the differences among individuals within populations. Compared with other endemic species on the Qinghai-Tibetan Plateau, O. curzoniae has a moderate level of the population genetic structure, which is higher than birds and lower than lizard, due to its limited dispersal ability.