The present study was aimed at examining the roles of altitude and temperature on body mass regulation in Eothenomys miletus from different areas of Hengduan mountain region in different seasons. Body mass, resting metabolic rate (RMR), nonshivering thermogenesis (NST), food intake, serum leptin levels and hypothalamic neuropeptide Y (NPY), agouti aelated peptide (AgRP), pro-opiomelanocortin (POMC), cocaine and amphetamine regulated transcript (CART) expressions were measured. The results showed that body mass and serum leptin levels were lower significantly in winter than that of in summer in five areas. But thermogenic characteristics and food intake were higher significantly in winter than that of in summer in five areas. NPY and AgRP expressions showed significant differences between two seasons, which were higher in winter and lower in summer, but POMC and CART expressions showed no significant differences between winter and summer from all areas. In summer, body mass and serum leptin levels had showed no significant differences among five regions, food intake, RMR, NST and NPY expressions were higher in higher altitude (Xianggelila, XGLL and Deqin, DQ) than that of lower altitude (Ailaoshan, ALS, Jianchuan, JC and Lijiang, LJ). In winter, body mass and serum leptin levels were lower, and food intake, RMR, NST, NPY and AgRP expressions were higher in XGLL and DQ. All of the results suggested that E. miletus can successfully overcome the physiological challenges of an cold temperature in winter by increasing thermogenic capacity, food intake and decreasing body mass and serum leptin levels. Higher altitude can reduce body mass, and increase thermogenic properties and NPY expressions. Differences changes of physiological regulation from five areas were observed in E. miletus, indicating that lower temperature and higher altitude may play an regulation on body mass and energy metabolism in E. miletus.