The O. sibirica (Orientallactaga sibirica), a member of the family Dipodidae, is widely distributed across Central Asia and plays a significant role in grassland ecosystems. While substantial ecological data on this species exists in China, research on intraspecific cranial variation is limited, and no extensive surveys have been conducted within its Chinese distribution range. This study aims to address this gap by capturing O. sibirica specimens from various geographical regions within China, conducting geometric morphometric analyses on their skulls, and examining the influence of current climatic conditions. Additionally, we predict changes in the suitable habitat areas for O. sibirica in China under future climate scenarios. Our results indicate that the major cranial variations in O. sibirica occur in the nasal, parietal, maxilla near the nasal end, zygomatic arch, and preorbital bridge. These features result in skulls from northeastern China clustering furthest from those in the Qinghai-Tibet Plateau. Skull size is primarily influenced by precipitation, whereas skull shape is affected by longitude, altitude, and temperature. Under future global changes, the suitable habitat for O. sibirica is likely to shrink, with the distribution centroid shifting towards higher latitudes in a northeasterly direction. Our analysis reveals that the cranial morphology of O. sibirica exhibits divergent adaptation across different geographical regions, particularly in the Qinghai-Tibet region, which we suggest should be designated as a new subspecies. Concurrently, future global changes are anticipated to alter the extent of suitable habitats in China, necessitating proactive measures to prevent potential rodent outbreaks.