Abstract: To address the issues of coarse texture, color deterioration, and reduced storage stability caused by wheat bran in whole wheat alkaline noodles, wheat bran was modified using microwave treatment, xylanase hydrolysis, and a combination of both methods to investigate their regulatory effects on the quality of whole wheat alkaline noodles. Polyphenol oxidase (PPO) activity was used as an indicator to select the optimal modification process. The modified wheat bran was then recombined to prepare whole wheat flour, whole wheat alkaline dough, and fresh whole wheat alkaline noodles. The effects on the physicochemical properties of whole wheat flour, as well as the rheological and textural properties, cooking performance, and storage stability of whole wheat alkaline dough and fresh whole wheat alkaline noodles, were comprehensively evaluated. The results indicate that microwave treatment significantly inhibits PPO activity in whole wheat flour, improves flour quality characteristics, and enhances dough viscoelasticity, hardness, and chewiness, thereby optimizing dough processing performance. Enzymatic hydrolysis and combined treatments increase the antioxidant capacity of whole wheat flour but exert limited effects on flour quality and dough rheological properties. In whole wheat fresh wet alkaline noodles, microwave treatment improves cooking properties and texture, while all treatments enhance noodle extensibility and resilience. Storage experiments show that the microwave-treated group exhibits lower PPO activity, higher L* values, delayed browning, and significantly improved storage stability. In summary, enzymatic hydrolysis and combined treatments are advantageous for enhancing antioxidant capacity and improving textural properties, whereas microwave treatment is most effective in improving whole wheat flour quality, enhancing dough processing performance, and elevating the overall quality of fresh whole wheat alkaline noodles.