Abstract: To mitigate the adverse effects of wheat bran-germ on the processing quality of whole wheat flour as well as on the cooking and storage quality of whole wheat alkaline noodles, six modification methods were employed. These methods included microwave, atmospheric pressure steam, enzyme digestion (xylanase), atmospheric pressure combined with microwave, atmospheric pressure combined with enzyme digestion, and microwave combined with enzyme digestion. The treated wheat bran-germ was reintegrated into core flour to prepare whole wheat dough and whole wheat alkaline noodles. The impact of these modification techniques on the quality of whole wheat dough and whole wheat alkaline noodles was evaluated by analyzing basic physicochemical indices of the whole wheat flour, rheological properties of the dough, and the cooking characteristics of the noodles, including textural and stretching properties, digestive properties, and storage stability. The results demonstrated that the microwave combined with enzymatic digestion group exhibited the highest protein content and the lowest dietary fiber content. Compared to the untreated group, the tanδ values of all six modified treatments decreased, indicating improved integrated viscoelasticity of the dough. The whole wheat alkaline noodles prepared with the microwave combined with enzymatic digestion treatment displayed the lowest hardness, optimal elasticity, minimal cooking loss, and superior tensile properties relative to other modified groups. Moreover, the starch hydrolysis rate of noodles from the atmospheric pressure steam combined with enzyme digestion and microwave combined with enzyme digestion groups was lower than that of other treatments, demonstrating enhanced resistance to digestion. During storage, all modified treatments effectively delayed microbial growth and reduced the activity of lipoxidase and peroxidase. Among these, the enzyme digestion and its combined treatment groups exhibited the longest storage duration. In summary, the microwave combined with enzyme digestion treatment of wheat bran-germ significantly enhanced the processing quality of whole wheat flour while markedly improving the cooking and storage quality of whole wheat alkaline noodles.