The high-throughput amplicon sequencing technology was used to study the microbiota of the the traditional fermented whole grain Tianpei from the typical regions of our country. The correlations between the bacteria communities and the properties of Tianpei were also analyzed. The results showed that Firmicutes were most abundant. At genus level, the abundance of Weissella, Lactobacillus and Staphylococcus was the highest ones. Principal coordinate analysis (PCoA) showed that the compositions of bacterial community among three kinds of Tianpei were different. According to Lefse analysis, the related biomarkers were found in each Tianpei, including Lactobacillus and Staphylococcus. By the distance-based redundancy analysis (db-RDA), it is illustrated that the bacterial community of Tianpei was significantly correlated with the properties of Tianpei (lactic acid, flavone, amino acid, protein, starch, free fatty acid and reducing sugar content). The prediction of bacterial functions in Tianpei based on 16S rDNA mainly involved in amino acid transport and metabolism and carbohydrate transport and metabolism etc. This study laid a theoretical foundation for the exploration of microbial resources of traditional whole grain fermented food, the improvement of the quality of Tianpei and the industrial production etc. It also could provide a reference for the research on the microbiota of other fermented foods.