Objective: To understand the characteristics of the microbial flora in Karez Xinjiang. Methods: Four different kinds of drinking water from Karez in Turpan, Xinjiang were collected, and they were sequenced using Illumina-Hiseq high-throughput sequencing technology. Majiorbio Shengxin Cloud Platform was used to analyze the diversity of microbial community structure. Results: After quality control, there were 446 700 effective bacterial sequences and 407 376 effective fungal sequences. A total of 2 586 OTUs were obtained based on 97% identity. At the phylum level, Proteobacteria was the common dominant bacteria phyla of the four samples. At the genus level, the common dominant bacteria of the Amur karez well (sample A) and the Awut karez well (sample T) were belong to the genus Hydrogenophaga, which accounted for 34.31% and 57.66%, respectively. The dominant genus of Say karez (sample S) was Curvibacter, accounting for 36.33%. The dominant genus of Miyim aji karez (sample M) was an unclassified_of Comamonadaceae, accounting for 34.84%. Ascomycota of fungi was the common dominant phyla among the four samples; the dominant bacteria of samples S, M, and T were Olpidium, accounting for 15.77%, 31.84%, and 16.38%, respectively. The dominant genus of sample A is unclassified_k_fungi, accounting for 27.68%. Conclusion: The four samples have similarities in bacteria and fungi phyla, genus, and species levels, but also have the differences. Although fungi diversity is higher than bacteria, the species abundance is smaller.