Food fermentation is one of the traditional food processing and preservation methods. With the biological function of beneficial microorganisms and their enzymes, the nutrients in food are decomposed and transformed into the unique flavor and nutrients that food raw materials are not endowed with before fermentation. If there is a lack of understanding of the structure and composition of its microorganisms, the problem of food safety will be occurred in fermented food. Based on this, the application of data processing analysis method in the identification of microorganisms in fermented food is further studied, which can provide theoretical support and method reference for the identification of microorganisms in fermented food.