In this study, to enhance corn flour incorporated noodles, corn flour was treated by the addition of 16% quercetin followed by microwave irradiation at 320 W for 30 min before being used as a partial wheat flour substitute in noodles. The effect of combined quercetin-microwave treatment on the processing properties of corn flour and the quality and digestion characteristics of corn flour incorporated noodles was investigated. The results showed that the treated corn flour had lower breakdown and setback values. Texture analysis revealed that the combined treatment resulted in the lowest gel hardness (103.94 g) and the highest elasticity (0.95) of corn flour. The noodles added with the treated corn flour had higher hardness, elasticity, chewiness, and resilience, lower cooking loss, and shorter optimal cooking time compared with the noodles with untreated corn flour. In vitro digestibility tests indicated that the resistant starch content in corn flour treated by quercetin combined with microwave was 26.45%. Compared with the wheat flour noodles, the resistant starch level in the noodles with the treated corn flour increased by 47.96%. Overall, combined treatment with quercetin and microwave appears to be an effective strategy for improving the quality and processing characteristics of corn flour and its products, providing valuable insights for developing high-quality, easily processable corn-based foods.