Guyuan cattle are located in the transitional zone between the northwest and north of China, as well as near the transitional zone between the north and sout of China. As a result, Guyuan cattle inhabit a transitional zone between semi-arid and semi-humid climate, featured by warm, humid summers and cold, dry winters, where admixture between taurine and indicine cattle has occurred. Nucleotide diversity, breed-specific single-nucleotide polymorphisms, linkage disequilibrium decay and regions of homozygosity suggested that the genomic diversity of Guyuan cattle was intermediate between those of taurine and indicine cattle. The signatures of selection in Guyuan cattle with excess taurine ancestry are associated with reproduction, immunity, body length, cold climate adaptation, pigmentation, muscle development, residual feed intake, and fat deposition. The signatures of selection in Guyuan cattle with excess indicine ancestry are associated with disease-resistance. Our study increases the understanding of the genetic resources of Guyuan cattle in the transitional zone between semi-arid and semi-humid region of China and provides valuable insights for genetic breeding programs that aim to leverage the breed complementarity and heterosis of taurine×indicine cattle.