Morphological variation stems from a number of sources, including environmental factors. The skull is the most complex part of animal skeleton. Studies on skull morphological variations can help uncover the taxonomic status of a species, age and other ecological characteristics of the populations. Qinghai-Tibetan Plateau (QTP) is a region with high degree of environmental heterogeneity and harbors a rich diversity of indigenous fauna. Plateau zokor belong to the genus Eospalax and are endemic to QTP. Zokors have a long evolutionary history that has resulted in specialized characteristics such as reduced eye size and sight, strong adaptation to hypoxia, and foreleg structure, and strong claws for digging. These make this species an ideal model for testing the role of environmental factors in shaping morphological features. The skulls of plateau zokor from eight geographical populations were collected from the northeast of QTP in Lintan, Tianzhu, Maqu, and Luqu of the Gansu Province. The morphometric measurements were taken and the geographic division of 13 morphological characteristics was compared and analyzed by a one-way analysis of variance and discriminant function analysis. The environmental influences on morphological differentiationwere discussed. The results indicated that there were significant differences in four morphological characteristics and highly significant differences in two morphological characteristics between the Lintan and Luqu groups, but there was only one significant morphological characteristic between the Maqu and Lintan groups, Lintan and Tianzhu groups, and Maqu and Luqu groups. Principal components analyses showed that the 13 main traits were represented by three principal components, and contributed to 96.981% of variations cumulatively stepwise discriminant function analysis showed the diastema length and total length had the greatest contribution to skull shape variation. A significant positive correlation between zokor skull size and altitude was detected. These findings suggested that geographical isolation and ecological conditions under the influence of altitude was the main factor shaping zokor skull differentiation.