Chinese chestnut is a Chinese characteristic economic forest fruit, and its planting area and output in China ranked in the world’s top. It is favored by consumers as one of the most important snack foods and food supplements. However, the content of starch in chestnut is relatively high. After processing, the content of fast-digested starch is significantly increased, which can easily lead to blood glucose disorder and can increase the risk of chronic metabolic diseases such as type 2 diabetes and obesity. In addition, chestnut starch is easy to suffer retrogradation during storage, which affects the processing quality of chestnut food. Therefore, to improve the nutritional function and processing quality of chestnut-based products, chestnut starch was modified by heat-moisture treatment (HMT) together with the composition of polyphenols. The effects of structure of caffeic acid (CCA)/chlorogenic acid (CGA) on the multi-scale structure, digestion and retrogradation performance of chestnut starch-polyphenol complexes were studied by modern analytical technologies. The results show that the addition of CCA/CGA during HMT can significantly reduce the digestibility of chestnut starch. And the content of anti-enzymatic components of chestnut starch, HMT treated chestnut starch, starch-CGA complex and starch-CCA complex are 15.53%, 17.77%, 19.72% and 22.73%, respectively. Moreover, as compared with CGA, small molecular volume of CCA is more likely to form anti-enzymatic hydrolysis structure domains (short-range ordered structures and V-type crystalline structures) with chestnut starch. Low temperature storage for 7 days can promote the retrogradation of chestnut starch granules and its polyphenol complexes. During the retrogradation process, the aggregation and re-arrangement of starch molecular chains will promote the formation of more ordered short-range ordered structures and crystalline structures, but the whole retrogradation is not obvious.As compared with HMT treated chestnut starch, the addition of polyphenols can hinder the aggregation and rearrangement of starch molecular chains to form long-range ordered crystalline structures, therefore inhibiting the retrogradation of starch granules and improving their storage stability. Overall, as compared with CGA, the addition of CCA can endow chestnut starch with great anti-digestion and anti-retrogradation performance, thus providing a new way and technical support for creating high quality and healthy chestnut starch food.