Environmental temperature serves a major driver for adaptive changes in wild organisms, however, its role in domestication has been less characterized. To uncover the mechanisms of cold tolerance in domestic animals, we sequenced genomes of 28 cattle at median coverage from warm and cold areas across China. By characterizing the population structure and demographic history, we identified two genetic clusters, i.e., northern and southern cattle groups, and a common historic population peak at 30 kilo years ago. Genome scan of cold tolerant breeds revealed genes that under selection sweeps enriched in thermogenesis related pathways. Specifically, we determined a substitution of PRDM16 (p.P779L) in north cattle, which maintains the formation of brown adipocytes through boosting expression of thermogenic related genes, indicating a vital role of this gene in cold tolerance. The findings provide a basis of genetic variations in domestic cattle that shaped by temperature environments and highlight a role of reverse mutation in livestock species.