Deoxynivalenol (DON) is a secondary metabolite produced by Fusarium fungi, which is found in a wide range of agricultural products, especially in wheat, barley, oat and corn. In this study, the distribution of DON in the wheat kernel and the effect of exposure time to ozone on DON detoxification were investigated. A high concentration of toxin was found in the outer part of the kernel, and DON was injected from the outside to the inside. The degradation rates of DON were 26.40%, 39.16%, and 53.48% after the samples were exposed to 75 mg/L ozone for 30, 60, and 90 min, respectively. The effect of ozonation on wheat flour quality and nutrition was also evaluated. No significant differences (P > 0.05) were found in protein content, fatty acid value, amino acid content, starch content, carbonyl and carboxyl content, and swelling power of ozone-treated samples. Moreover, the ozone-treated samples exhibited higher tenacity and whiteness, as well as lower extensibility and yellowness. This finding indicated that ozone treatment can simultaneously reduce DON levels and improve flour quality.