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In the current research, samples of yak gastrointestinal tracts (GITs) were used to profile the bacterial compositional characteristics using high through-put sequencing technology of 16S RNA amplicon. A total of 6959 OTUs was obtained from 20,799,614 effective tags, among which 751 OTUs were shared by ten sections. A total of 16 known phyla were obtained in all samples—the most abundant phyla were <i>Firmicutes</i> (34.58%), <i>Bacteroidetes</i> (33.96%) and <i>Verrucomicrobia</i> (11.70%). At the genus level, a total of 66 genera were obtained—<i>Rikenellaceae_RC9_gut_group</i> (7.24%), <i>Akkermansia</i> (6.32%) and <i>Ruminococcaceae</i>_UCG-005 (6.14%) were the most abundant. Species of Observed (Sob), Shannon and Chao values of the Stomach were the greatest, followed by the large intestine, while small intestine had the lowest diversity (<i>p</i> < 0.05). <i>Bacteroidete</i> were more abundant in sections from rumen to duodenum; while Firmicutes were the most abundant in sections from jejunum. ABC transporters (7.82%), Aminoacyl-tRNA biosynthesis (4.85%) and Purine metabolism (3.77%) were the most abundant level-3 pathways in all samples. The results of associated correlation analysis indicated that rectum samples might be used as an estimator of rumen bacterial communities and fermentation. The results of this research enrich the current knowledge about the unique animals of the QTP and extend our insight into GITs microecology of various animals.