Eothenomys were the inherent species in Hengduan Mountains region, which had special status in Microtus, Arvicolinae. In order to investigate the geometric morphometrics of the craniums and mandible in nine species of Eothenomys (E. fidelis, E. melanogaster, E. chinensis, E. proditor, E. custos, E. cachinus, E. eleusis, E. miletus and E.olitor), ANOVA analyses, principal components analysis, thin plate spline, UPGMA and Multidimensional Scaling were used. The results showed that there had significant differences in skull shapes of centroid size in Eothenomys. Orbital cavity and alveolar region had significant differences in intraspecific skulls, some differences were shown in interspecific skulls, such as the point between the anterior tip of suture nasal and premaxilla, anterior tip of suture between nasal and premaxilla, anterior and posterior most ventral points of the upper incisor alveolus, and coronoid process, angular process ascending ramus and condylar process on the mandible. The genus Eothenomys could be classified into two subgenera. Moreover, it was inferred that the varieties of skulls characteristics in E. miletus, E. eleusis, E. cachinus and E. melanogaster were main influenced by temperature and humidity; E. olitor, E. custos and E. chinensis were main influenced by diet. Thus, the environmental factors (temperature, humidity and diet) may lead to the difference of geometric morphometry of skulls characteristics in Eothenomys.