Background: Exploring thermoregulation and metabolic characteristics responses to high altitudes is important for understanding ectothermic animal high-altitude adaptation mechanisms. However, how could these species compensate for adverse environmental impacts are controversial and poorly understood. In the present study, the selected body temperature, mitochondrial consumption, proton leak and enzyme activity of a lizard Phrynocephalus vlangalii from different altitudes (Maduo and Golmud, with altitude at 4270 and 2750 m, respectively) were analyzed to investigate the thermoregulatory and metabolic regulation strategies of this native high-altitude lizard at Qinghai-Tibet Plateau.Results:The results indicated that the Maduo population had a faster heating rate and selected significantly lower body temperatures than those of the Golmud population. The mitochondrial oxygen consumption rates in both the liver and skeletal muscle of the Maduo population were significantly lower than those of the Golmud population, but the thermal sensitivity of skeletal muscle mitochondrial in Maduo population was significantly lower than that in Golmud population. The proton leak of liver mitochondria in the Maduo population account for a lower percentage of state III than that of the Golmud population (11.4~14.6% VS. 22.5~25.1%), which indicate a higher ATP production in liver mitochondria. The results of three enzyme activities reflect significant both tissue- and population specificity. Especially, a low ratio of LDH/CS and HOAD/CS in the liver of the Maduo population indicating that metabolism of the liver mainly depended on aerobic metabolism and especially the use of carbohydrate as a metabolic substrate in Maduo population.Conclusions: These distinct variable characteristics between two populations of P. vlangalii could be considered important strategies in thermoregulation and metabolic regulation for living at different altitudes and could be especially necessary for lizards to effectively compensate for the negative influence of cold and hypoxia at high altitude.