The Tibetan macaque (Macaca thibetana) is an endemic macaque species in China belonging to the sinica group in genus Macaca. Here, we report the first chromosome-level genome assembly for the Tibetan macaque using PacBio long-read sequencing and Hi-C technology. The assembled Tibetan macaque genome was 2.82 Gbp in size with contig N50 of 48.75 Mbp and scaffold N50 of 150.62 Mbp, which was anchored to 22 chromosomes. Compared to the chromosome-level genome of rhesus macaque and cynomolgus macaque, the genome size of the Tibetan macaque is the smallest and the assembly quality is the best. A total of 22,485 protein-coding genes and 1.33 Gbp repeat sequences were annotated in the Tibetan macaque genome. Phylogenetic analysis indicated the Tibetan macaque was closely related to the stump-tailed macaque and diverged from a common ancestor 5.06 million years ago. A total of 977 positively selected genes were identified, which were enriched in pathways related to the thyroid, diabetes mellitus, fatty acid biosynthesis and metabolism. Among them, 11 genes associated with tail development and 9 genes associated with body size were found to be under positive selection, which might contribute to short tail and large body size of the Tibetan macaque. The structural variation (SV) analysis between the Tibetan macaque and other macaques identified 6,778 Tibetan macaque-specific SVs. Among them, three deletions and four insertions in six genes might be associated with tail development and body size. The high-quality genome of the Tibetan macaque will benefit further biological and evolutionary studies on primates.