Objective To investigate the effect of hypobaric hypoxia and cold exposure on brown adipose tissue in mice. Methods Twenty-four 6-week old SPF C57BL/6 male mice were randomly divided into 4 groups with 6 mice in each group:normal atmospheric pressure and temperature group (18~22℃, 20~60 m)(NTNP), low atmospheric pressure and normal temperature group(18~22℃, altitude of 5000 m)(NTLP), normal atmospheric pressure and cold exposure group(0~6℃, altitude of 20~60 m)(LTNP), low atmospheric pressure and cold exposure group(0~6℃, altitude of 5,000 m)(LTLP). The experimental period was 4 weeks. The body weight was measured at the beginning and end of the experiment. By the end of the four-week trial, the back and inguinal fat were dissected and observed by histology using HE staining. The expression of UCP-1 as the marker of brown adipose tissue in the back fat was detected by qPCR and western blot. Results The body weight gain of NTNP group was higher (P< 0.05) than the other three groups. Meanwhile, the color of the back and groin fat tissue of mice of LTNP and LTLP groups were darker, the blood supply in mice of these two groups was richer than the NTLP group. The volume of adipose tissue of NTNP group was higher than others. The histology showed that the back adipose cells of the mice were smaller and darker and full of multilocular lipid droplets, exhibiting a typical morphology of brown fat cells. Compared with the NTNP and NTLP groups, the mRNA and protein levels of UCP-1 were higher under cold exposure, while low atmospheric pressure had a tendency to reduce the mRNA expression of UCP-1. Conclusions The formation of brown fat is affected by the imitated conditions of low atmospheric pressure and cold exposure, and is more closely related to the decresed temperature.