The purpose of this study was to utilize the monascus pigments (MPs) for the production of functional wheat noodles. The cooking properties, texture characteristics, and microstructure of dried noodles containing MPs were investigated. The underlying mechanisms of the impact of MPs on noodles were studied. After adding MPs, noodles' water absorption, broken rate, and cooking loss increased, while the optimal cooking time and textural characteristics were reduced. SEM demonstrated that MPs weakened the gluten network, leading to uneven exposure of starch to the network. Moreover, thermal qualities (endset temperature and enthalpies) increased while pasting characteristics (setback, peak, trough, and final) decreased after incorporating MPs with wheat flour. The short-range ordered structure (R1047/1017: 0.616 to 0.750 and R994/1017: 2.229 to 2.435) and the long-range ordered structure (crystallinity: 11.87%–13.59%) of starch showed an increase with the MPs addition. Additionally, MPs decreased the gluten's β-sheet and α-helix but increased the random coil. The structural alterations in the starch and protein of the noodles were correlated with textural properties. Therefore, noodles with 0.5%∼1.0% MPs exhibited acceptable qualities. This study provided references for the development of functional wheat-related products.