Ecology influences the process of speciation. The interspecific differences in mammalian skull morphology, induced by environmental factors, are important when investigating speciation. In the Qinghai–Tibetan Plateau, the genus Eospalax consists of six species of subterranean rodents, each with its unique niche, making it an ideal model for studying the relationship between biological evolution and the environment. Here, the interspecific differences in five of the six extant species (E. cansus, E. baileyi, E. rufescens, E. smithii, and E. fontanierii) were evaluated at the morphometric and ecological levels using geometric morphometrics, a powerful tool for studying morphological variation. The multivariate analysis of variance showed significant differences in skull morphology on the dorsal and ventral sides in all species. The thin‐plate splines showed that the variations in skull morphology were primarily in the infraorbital foramen, frontal bone, zygomatic arch, occipital bone, incisors, incisive foramen, and tooth row. The multivariate regression analysis showed a significant positive correlation between skull morphological variations and ecological factors; precipitation accounted for the more variations than altitude and temperature. Species inhabiting regions with the highest altitude, minimum precipitation, and temperature (E. baileyi) had the largest infraorbital foramen and zygomatic arch, shortest occipital bone and widest frontal bone, smallest angle formed by two incisors, and longest incisive foramen. Our study elucidates the relationship between skull morphological differentiation and environmental factors in Eospalax, while the biological response to the environment detected warrants further investigation. Our results can provide references for speciation at local environmental scale.