To improve the physicochemical properties and processing performance of black wheat flour dough, the effects of adding Glucose oxidase (GOD) on the gelatinization, thermomechanics dough tensile, rheology properties, and microstructure of black wheat flour were investigated using a rapid viscosity analyzer, a texture analyzer, and a scanning electron microscope, among other methods. The effects were also explained in terms of changes in protein fractions. The results showed that the moderate addition of GOD could significantly reduce the content of free sulfhydryl groups and increase the content of disulfide bonds in the dough of black wheat flour, thereby enhancing the degree of protein cross-linking and significantly improving the physicochemical properties of black wheat flour dough. The best improvement in dough structure and properties was achieved when the GOD addition was 0.8%, at which point the ratio of wheat alcohol-soluble protein to wheat gluten (0.81) was close to the optimal ratio (1.0). This study has provided a certain reference for the development of black wheat-based foods and the improvement of their edible quality.