Melatonin (MEL) is an indole hormone synthesized and secreted by the pineal gland at night, which is involved in the regulation of body mass and thermogenesis in small mammals. To test the effects of exogenous MEL on body mass and thermogenic ability in two different red-backed vole (Eothenomys miletus) populations from two different regions (Kunming [KM] and Dali [DL]) with different annual variation in climatic variables, such as temperature, sunshine and rainfall. we traced the changes of energy balance in E. miletus from KM and DL, which were placed at 25 ± 1°C with photoperiod of 12 L:12 D, intraperitoneal injection of MEL was performed daily for 28 days. The results showed that body mass and food intake were significantly decreased, while resting metabolic rate (RMR) and nonshivering thermogenesis (NST) were significantly increased after MEL injection; Contents of total protein, mitochondrial protein, the activities of cytochrome C oxidase (COX) and α-glycerophosphate oxidase (α-PGO) in liver and brown adipose tissue (BAT) were enhanced; the activity of thyroxin 5′-deiodinase (T 4 5′-DII) and uncoupling protein 1 (UCP1) in BAT were also increased. Serum leptin, triiodothyronine (T 3 ) levels and T 3 / T 4 ratio were significantly increased, thyroxine (T 4 ) levels was significantly decreased. Moreover, body mass and food intake in E. miletus from KM were higher than those from DL, but RMR and NST were lower than those from DL.Changes of body mass, food intake and thermogenic activity of KM were higher than those of DL when exposed to injection of MEL, indicating that E. miletus in KM were more sensitive to MEL. Furthermore, MEL was involved in the regulation of body mass and thermogenesis in E. miletus between KM and DL.