The invention provides a processing method of voitoxin-containing wheat and application. The method comprises the following steps of (1), inoculating bacillus subtilis, saccharomyces cerevisiae and bacillus licheniformis in a culture medium and culturing to obtain mixed biological bacterial broth; (2), milling the wheat to obtain bran and flour; (3), adding the mixed biological bacterial broth anddiatomite into the bran and carrying out aerobic fermentation to subsequently obtain fermented bran and fermentation broth; (4), water-scrubbing the flour to subsequently obtain wet gluten and starchmilk and carrying out yeast fermentation on the starch milk to subsequently obtain alcohol; (5), adding the fermentation broth into alcohol waste vinasse broth after the alcohol is distilled, so thata biological microbial inoculum is prepared. The method is used for quickly decomposing voitoxin in the bran by adopting the mixed biological bacterial broth and enriching the voitoxin in the flour in the alcohol waste vinasse broth, and is used for culturing the mixed biological bacterial broth and obtaining the biological microbial inoculum for degrading the voitoxin.