In arid ecosystems, precipitation and temperature are two key factors, with altitude further shaping habitat conditions through its regulatory effects on temperature. These environmental variables interact with habitat resource distribution, which significantly affects animal morphology, behavior, and ecological interactions, including food availability, body size, migration patterns, competitive dynamics, and shelter utilization. However, existing research predominantly focuses on small-scale and localized climatic impacts, lacking comprehensive explanations for large-scale, with multiple ecological responses. As a widely distributed rodent in arid environments, Orientallactaga sibirica serves as an effective bioindicator of climate and habitat resource variations. This study investigates the effects of climate change and habitat resource heterogeneity on O. sibirica by analyzing its body size and trophic niche through field surveys and stable isotope techniques. Climate data, altitude, and fractional vegetation cover (FVC) were integrated to explore the underlying mechanisms driving these variations. The results reveal significant variability in O. sibirica body size across different habitat conditions. Individuals inhabiting the mid-temperate semi-humid zone, the plateau temperate semi-arid zone, and high-altitude regions exhibited significantly larger body sizes compared to those in other climatic regions. Body size demonstrated a significant linear decline with increasing mean annual temperature, while it exhibited a significant linear increase with rising altitude, annual precipitation, and FVC. The trophic niche width of O. sibirica varied across habitat types, being widest in the warm-temperate semi-humid zone and at mid-altitudes. Segmented structural equation modeling revealed that elevation and mean annual temperature exerted significant negative effects on O. sibirica body size by affecting FVC, whereas annual precipitation had a significant positive effect on body size, mediated through FVC. These results highlight the complex interactions between climatic factors and habitat conditions in shaping the morphological and ecological adaptations of O. sibirica, providing valuable insights into species responses to environmental change in arid ecosystems.