In order to develop and improve the utilization of whole grains, the macrogenomics method was used to analyze the structural composition of the whole wheat traditional fermentative dough, and the result shows that the core fermentation genus was Lactobacillaceae Lactobacillus brevis. According to the relevant literature, the flavor substances of whole wheat traditional fermentative dough and commercial fermentative dough were determined. The traditional fermentative dough contains 9 more flavor substances than commercial fermentation and there were also differences in the content, with the hydrocarbon content was showing the highest. It was indicated that the traditional fermentation strain was more conducive to the formation of flavor substances in the whole wheat dough, this was more acceptable to consumers and provided theoretical support for the application of traditional fermentation strains in whole wheat products.