In order to find out the differences in the microbial community structure in Qula at different altitudes of Tibet, a total of 40 yak Qula samples were collected from three groups at low, middle and high altitude for high-throughput sequencing. The results showed that there were differences in microbial community diversity among the different groups of samples. With the increase in altitude, the diversity and richness of bacterial flora in Qula samples showed a downward trend, and so did the abundance of fungal flora, while the diversity of fungal flora did not change significantly. The samples from the low, middle and high altitude groups contained 2411, 1391 and 1197 bacterial operational taxonomic units (OTUs), respectively, and 715 bacterial OTUs were common to the three groups; the dominant bacterial genera identified were Lactococcus and Lactobacillus, with an average relative abundance of 34.0% and 18.4%, respectively. The samples from the low, middle and high altitude groups contained 801, 343 and 399 fungal OTUs, and 173 fungal OTUs were common to the three groups; the dominant fungal genus identified was Geotrichum, with an average relative abundance of 33.8%. The results of this study can provide a theoretical basis for the selection and utilization of characteristic microbial resources in Qula.