The structure of prokaryotic microbes in fermented grains during the brewing of cotton sweet type liquor was analyzed by the high through put sequencing technology.Two kinds of cellar pools were selected to track the fermented grains with different space positions and different fermentation stages in the cellar. The samples of the mixed fermented grains were packed in a sterile vacuum plastic bag, and DNA extraction and subsequent high through put sequencing analysis were carried out. The results showed that the similarity of the prokaryotic microorganism in fermented grains of No. 1 pit cellar and No. 2 pit cellar was relatively high based on the operational taxonomic units (OTU) analysis. The species similarity of prokaryotic microorganisms in the same pit was very high. At the same time, the species of bacteria in fermented grains in the two pits were decreased with the fermentation.From the sample type, the diversity of prokaryotic microbes in fermented grains of pit No. 1 was higher than that of the prokaryotic microorganism in fermented grains of No. 2 pit cellar.There were similar types of prokaryotic microbial flora in fermented grains of No. 1 and No. 2 pit cellar. The dominant bacteria in the fermented grains of No. 1 pit and No. 2 pit were Firmicutes, Cyanobacteria, Proteobacteria, Actinobacteria, and Gemmatimonadetes. The number of dominant bacteria gates was in order of:Firmicutes, Proteobacteria, Actinobacteria, Cyanobacteria, Gemmatimonadetes.