Microorganisms have been used for the production of fermented food products, such as cheese, sourdough, beer, wine, and vinegar. By transforming raw materials into value-added products with superior flavor, texture, and longevity, humans have enjoyed the benefits of this biotechnology. Microorganisms genome editing can optimize the metabolic pathways and phenotypes of the most familiar industrial microorganisms, greatly improve the production traits of the strains and shorten the breeding cycle. At present, a lot of technologies have been used in the transformation and improvement of industrial microbial strains, showing a good application prospect in the process of breeding strains. In addition, microorganisms genome editing has also been widely applied in pharmaceutical and environmental.