There are many lakes in Xinjiang, but nearly half of the lakes have evolved to the stage of salt lake development because of the strong salt formation effect in arid climate. The different salt lakes contain rich resources of halophilic and halotolerant microorganisms. In order to better acquire the distribution of microbial resources and the response to environmental factors of salt lakes in Xinjiang, the bacterial and archaeal diversities of five salt lakes bottom sediment at different evolutionary stages of Xinjiang Tianshan north slope. The main driving factors were studied using the high-throughput sequencing technique in this paper to reveal the pattern of microbial community structure change during the salt lake evolution process. The sediment samples from the bottom of five salt lakes were collected, the sediment properties were tested, and the bacterial and archaeal 16S rRNA gene were sequenced. In the five salt lakes, the differences of sediment properties and microbial community structure were compared and the correlation of microbial richness and environmental factors sediment was analyzed. The results showed that the order of total salt and Na⁺ content in the bottom sediments of the five salt lakes was Barkol lake > Yiwu lake > Ebinur lake > Yanhu lake > Chaiwobao lake. The sediments of other four salt lakes are alkaline except Ebinur lake. Alpha diversity displayed that the bacterial richness, chao1, ACE and Shannon richness indexes of the five salt lakes were all higher than the corresponding richness indexes of archaea. The diversity of bacterial richness indexes was greater than that of archaeal richness indexes in these lakes. Through the annotation with sliva database, the bacterial and archaeal communities containing 58 phyla, 68 classes, 138 orders, 253 families, 560 genera and 4 phyla, 8 classes, 12 orders, 21 families, 60 genera, respectively, were found in the bottom sediments of the five salt lakes, in which Proteobacteria was the main phylum of bacteria and Euryarchaeota was the main phylum of archaea. The dominant genus of bacteria and archaea in different salt lakes are different, for example, Barkol lake was mainly some halophilic and halotolerant bacterial genus and Yiwu lake was mainly some halophilic and halotolerant archaeal genus. The PCoA analysis results also demonstrated that the different salt lakes had their unique microbial community structure at the operational taxonomic units (OTUs) level. The results of RDA and Bioenv analysis showed that the microbial community structure in the sediments of the salt lake bottom was mainly affected by the Na⁺ and total salt concentration, while the archaeal community might be regulated by many physical and chemical factors. Moreover, the special brine components of the salt lake would have a significant impact on the microbial community structure.