Abstract: Quinoa is one of the most popular ingredients in the creation of healthy and environmentally friendly foods, due to its rich nutrient composition, balanced amino acids, and various bioactive substances. Quinoa noodles can be prepared for green and healthy food, particularly for better taste and market prospects. However, the traditional processing of wheat noodles cannot fully meet the high quality of quinoa noodles at present, due to the lack of gluten. Among them, extrusion has been applied to prepare the whole quinoa noodles. The natural color of food can also be closely related to its nutritional value. Quinoa grains with different colors often vary in the content of starch, protein, fat, fiber, and active substances. This study aims to clarify the great influence on the cooking and nutritional quality of extruded noodles made with quinoa as raw materials. The mechanism of quality of extruded quinoa noodles with different colors was explored to compare the basic components, gelatinization of quinoa flours, the microstructure, cooking quality, active components, and starch digestion. Results showed that the white quinoa achieved the highest content of total starch and crude fiber, compared with the red and black quinoa powder. The content of crude fiber increased significantly with the deepening of the color of quinoa powder. Among the three types of quinoa powder, the red quinoa exhibited the highest levels of fat and protein content. In terms of gelatinization properties, the peak viscosity, final viscosity, and setback value of white quinoa powder were superior to those of red and black quinoa powder. The pasting temperature of white quinoa powder was lower than that of red and black quinoa powder. Furthermore, L* values significantly decreased after extrusion, whereas, a* value and b* values significantly increased (P < 0.05). Additionally, the red and black quinoa powder, along with their extruded noodles, exhibited higher levels of polyphenols, flavonoids, and antioxidant activities, compared with the white quinoa. X-ray diffraction revealed that the extrusion process caused the changes of starch crystal type from type A to V. There was a decrease of starch crystallinity in the white, red, and black quinoa noodles from 17.12%, 25.55%, and 21.41% to 10.53%, 8.06% and 7.71%, respectively. White quinoa noodles shared the highest crystallinity, due to the high starch content and high setback value of powder. The recrystallization of starch formed a relatively stable and orderly molecular structure, thus enhancing the crystallinity of starch in the extruded quinoa noodles. Although the cooking time of red and black quinoa extruded noodles was shorter than that of white ones, their overall cooking quality was notably inferior. The cooking loss of white quinoa noodles was 7.46%, which was significantly lower than that of red (10.12%) and black (9.16%). At the same time, the extruded white quinoa noodles also exhibited the highest hardness (30.71 N) and springiness (0.97). The extruded noodles relied primarily on the gelatinization and retrogradation of starch. The rearrangement of starch was dominated to form a stable gel structure after extrusion for the cooking quality of extruded quinoa noodles. Scanning electron microscope images confirmed that the gel network structure of white quinoa extruded noodles was denser and more complete, thereby leading to the lower cooking loss and superior texture, compared with the red and black quinoa extruded noodles. The in vitro starch digestibility showed that the white quinoa noodles contained the highest resistant starch content and the lowest predicted glycemic index of 68.56. In summary, the red and black quinoa presented a relatively higher content of active substances, but white quinoa was more suitable for the production of high-quality and low-GI extruded noodles. This finding can provide the theoretical and technical reference for the production and processing of high-quality quinoa noodles.