In order to explore differences of body compositions and digestive tract morphology in Eothenomys miletus from Hengduan Mountains at different areas. Samples wre collected from five sites from the north to the south: Deqin, Shangri-La, Lijiang, Jianchuan and Ailao Mountain. Body mass, wet and dry masses of body components (including heart, lung, liver, spleen and kidney), masses and lengths of stomach, small intestine, large intestine and cecum were measured in the present study. The results showed that body mass was significantly different among the five different areas (F=3.895, P<0.05); from lightest to heaviest:  Deqin, Shangri-La, Lijiang, Jianchuan and Ailao Mountain. There were significant differences in wet mass of liver among different sites (F=3.895, P<0.05), with heaviest coming from the Deqin population, and teh lightest fromthe Ailao Mountain population. Length of stomach showed significant differences among five areas (F=3.04, P<0.05), being significantly larger in Ailao Mountain in E. miletus. All of the above results showed that body mass, wet mass of liver and morphology of the gastrointestinal tract had significant differences that may be related to the gradual transition of environmental factors in Hengduan Mountains. In conclusion, E. miletus in different areas from Hengduan Mountains adapt to differing climate and environment conditions mainly by changing their body mass, organ masses and digestive tract morphology.