Morphological characteristics are closely related to habitat characteristics; habitat differences drive morphological differentiation, resulting in intraspecific and interspecific differences. In the present study, it was shown that body mass and body length in Eothenomys miletus from five regions: (Dali (DL), Jianchuan (JC), Lijiang (LJ), Xianggelila (XGLL) and Deqin (DQ)) of Hengduan Mountain, showed differentiation in bone morphological indices. The length of the sternum in E. miletus in JC is smaller than that in XGLL, and the length of the lumbar vertebrae is smaller than that in XGLL and DQ. The length of other trunk bones and limb bones of E. miletus in DL, JC and LJ at low latitudes and high temperatures were longer than in XGLL and DQ at high latitudes and low temperatures. Principal component analysis associated XGLL and DQ populations and cluster analysis divided the populations from five regions into two categories. The increase in bone length and mass correlated with increased body mass in E. miletus. Change in bone length does not conform to Bergmann's Law, which was affected by altitude, average annual temperature and latitude. Moreover, food, terrain, and living habits may also affect bone morphology in E. miletus.