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Disturbances, both human-induced and natural, may re-shape ecosystems by influencing their composition, structure, and functional processes. Plateau zokor (Eospalax baileyi) is a typical subterranean rodent endemic to Qinghai-Tibetan Plateau (QTP), which are considered ecosystem engineers influencing the alpine ecosystem function. It is also regarded as a pest aggravating the degradation of overgrazed grassland and subject to regular control in QTP since 1950s. Climate change has been predicted in this region but little research exists exploring its impact on such subterranean rodent populations. Using plateau zokor as a model, through maximum entropy niche-based modeling (Maxent) and sustainable habitat models, we investigate zokor habitat dynamics driven by the future climate scenarios. Our models project that zokor suitable habitat will increase by 6.25% in 2050 in QTP. The predication indicated more threats in terms of grassland degradation as zokor suitable habitat will increase in 2050. Distribution of zokors will shift much more in their southern range with lower elevation compare to northern range with higher elevation. The estimated distance of shift ranges from 1 km to 94 km from current distribution. Grassland management should take into account such predictions in order to design mitigation measures to prevent further grassland degradation in QTP under climate change scenarios.