Sleep deprivation (SD) can affect the adaptive thermogenesis in laboratory rodents, but the molecular mechanism and the crosstalk with other organs remain largely unknown. In order to investigate the effects and mechanisms of SD on thermoregulation and energy metabolism, here we measured the changes of body weight, body fat mass, body temperature, resting metabolic rate (RMR), and thermogenic gene expression in brown adipose tissue (BAT), white adipose tissue (WAT), skeleton muscle and liver in C57BL/6J mice during 7-day SD with rotating rod sleep deprivation device. Results showed that compared with the control group, the body weight and body fat mass of SD mice were decreased and RMR of SD mice increased. The gene expression of Ampk, Pgc1α and Ucp1 which related to thermogenesis in BAT and WAT were significantly increased, and the expression of Ampk, Serca1, Serca2 and Ucp3 which related to thermogenesis in skeletal muscle were significantly increased in SD mice. Taken together, these data demonstrated that 7-day SD enhanced the adaptive thermogenesis in mice by activating AMPK, including the upregulation of the AMPK - PGC1α - UCP1 pathway in BAT, and the AMPK - UCP3 and SLN - SERCA pathway in skeleton muscle. Our data provide the molecular evidence for SD-stimulated adaptive thermogenesis and energy metabolism in small mammals.