Saline lakes represent a particularly interesting aquatic environment for harboring high microbial diversity. However, the microbial diversity in different states and locations of saline lake is often overlooked. We studied for the first time the diversity and relative composition of the microbial communities in the Chagan Lake, NE China, and investigated the differences in microbial species and physical and chemical factors in different geographical localities of the lake. After extracting the total DNA of the sample, we tested the library with the established library, sequenced the qualified library with Illumina HiSeq 2500, and studied the bacterial diversity by 16S rRNA targeted metagenomics analysis. Results reveal that the highest microbial abundance in Chagan Lake at genus level was Proteobacterium followed by Actinomycetes and Bacteroides . In addition, we compared the microbial composition within the lake using alpha- and beta-diversity indices, showing that both diversity and evenness were the highest in the middle of the lake and lowest in the west of lake areas, and in the upper, middle, and lower depth of water columns, the low water column had the highest species number in the whole water environment, but the difference was not significant. We believe that physicochemical factors contribute to the formation of microbial community composition and diversity. In aquaculture industry, it is impossible apply horticulture for making full use of the spatial differences in the microbial composition of the water. Therefore, combining cultured aquatic animal with the most suitable microbial species is a good way to boost the breeding effect for greater economic value.