[Objetive] Chaka Salt Lake is a famous natural and crystal salt lake on the Qinghai-Tibet Plateau, having unique halite deposits and abounding in edible salt. There are abundant halophilic bacteria resources and potential species in the salt lake environment. The community structure and species diversity of bacteria and archaea remains unknown. [Methods] Microbial community and diversity of water and sediment mixture samples were investigated by the 16S rRNA V3?V5 region gene based on an Illumina high-throughput sequencing platform. [Results] Totally 117 192 and 110 571 valid sequences of bacterial and archaeal 16S rRNA gene were generated respectively in this study. Results showed that the species annotation OTU (Operational taxonomic unit) numbers of bacteria and archaea were 421 and 317, respectively, belonging to definite taxonomic bacteria of 14 phylum 28 classes 170 genera and classified archaea of 5 phylum 4 classes 34 genera. Bacterial dominant groups were Firmicutes (68.37%), followed by Proteobacteria (20.49%). The bacterial dominant populations were Bacillus (41.94%), Oceanobacillus (8.03%), Pseudomonas (7.67%), Halanaerobium (7.42%) and Lactococcus (7.38%) in turn. Furthermore, archaeal dominant group was Halobacteria in the Euryarchaeota, and dominant archaea populations were Halonotius (17.21%) and Halorubrum (16.23%). [Conclusion] This study revealed the community structure and the species diversity of bacteria and archaea in Chaka Salt Lake. These results could provide significant theoretical references for the exploitation and utilization of microbial resource.