A novel starch-based model dough used to exploit staple foods was demonstrated to be feasible, which was based on damaged cassava starch (DCS) obtained by mechanical activation (MA). This study focused on the retrogradation behavior of starch dough and the feasibility of its application in functional gluten-free noodles. Starch retrogradation behavior was investigated by low field-nuclear magnetic resonance (LF-NMR), X-ray diffraction (XRD), scanning electron microscope (SEM), texture profile and resistant starch (RS) content analysis. During starch retrogradation, water migration, starch recrystallization and microstructure changes were observed. Short-term retrogradation could significantly alter the texture properties of starch dough, and long-term retrogradation promoted the formation of RS. The damage level influenced starch retrogradation, and damaged starch with the increasing damage level was beneficial to facilitate the starch retrogradation. Gluten-free noodles made from the retrograded starch had acceptable sensory quality, with darker color and better viscoelasticity than Udon noodles. This work provides a novel strategy for the proper utilization of starch retrogradation for the development of functional foods.