Abstract: With the increasing incidence of abnormal glucose metabolism diseases such as diabetes, it is of great significance to explore the structural characteristics (crystal structure, chemical bonds and functional groups) and physicochemical properties (thermodynamic properties, morphological characteristics and viscosity) of starch digestion products for the development of specific functional foods. Based on this, the dynamic human gastrointestinal digestive system model was used to simulate the oral, gastric and small intestinal digestion process of quinoa starch (QS) in vitro to explore the structural characteristics and physicochemical properties of digestion products at each stage. The results showed that the gastric half-emptying time of gelatinized QS was 29.53 min. The pH value of the stomach contents increased initially and then decreased, and the digestion characteristics were close to those of fluid food. After digestion in the oral cavity, stomach and small intestine, the crystal type of the product changed to V-type, and the weak crystalline starch continued to disintegrate. The crystallinity decreased, the crystal structure diversity increased, the resistance to enzymatic hydrolysis increased, the viscosity gradually decreased, and the starch was difficult to gelatinize. During the digestion process, no new chemical groups were produced, the hydrogen bond force gradually weakened, the glycosidic bonds and pyranose ring structure were broken. Furthermore, both the degree of double helical structure and crystallinity of starch molecules decreased, the transition temperature increased, and the melting enthalpy decreased. The digestion product was transformed into lamellar form, the surface damage increased, and enzymatic hydrolysis pores appeared in the small intestinal digestion product. Therefore, significant differences were observed in the crystal structure, functional group content, enzymatic hydrolysis characteristics, and surface morphology of QS digestion products during oral, gastric, and small intestinal digestion. The results of this study provide a theoretical basis and supporting data for promoting the research of quinoa-based foods and the development of slowly digesting functional foods.