Jinchuan yak, a newly discovered yak breed, not only possesses a large proportion of multi-ribs but also exhibits many good characteristics, such as high meat production, milk yield, and reproductive performance. However, there is limited information about its overall genetic structure, relationship with yaks in other areas, and possible origins and evolutionary processes. In this study, 7,693,689 high-quality single-nucleotide polymorphisms were identified by resequencing the genome of Jinchuan yak. Principal component and population genetic structure analyses showed that Jinchuan yak could be distinguished as an independent population among the domestic yak population. Linkage disequilibrium analysis showed that the decay rate of Jinchuan yak was the lowest of the domestic yak breeds, indicating that the degree of domestication and selection intensity of Jinchuan yak were higher than those of other yak breeds. Combined with archaeological data, we speculated that the origin of domestication of Jinchuan yak was ~6000 yr ago (4000–10,000 yr ago). The quantitative dynamics of population growth history in Jinchuan yak was similar to that of other breeds of domestic and wild yaks, but was closer to that of the wild yak. No significant gene exchange between Jinchuan and other domestic yaks occurred. Compared with other domestic yaks, Jinchuan yak possessed 339 significantly and positively selected genes, several of which relate to physiological rhythm, histones, and the breed’s excellent production characteristics. Our results provide a basis for the discovery of the evolution, molecular origin, and unique traits of Jinchuan yak.