The balance between inhibiting and promoting starch retrogradation is a challenge in developing low glycemic index foods, as they are important ways for preventing texture deterioration and reducing digestibility, respectively. Currently, a comprehensive analysis on how starch chain structures influence gel strength and digestibility through molecular rearrangement during retrogradation is still lacking. This paper reviewed the short-term and long-term retrogradation properties of amylose and amylopectin, and comprehensively discussed the roles of their chain structures in the ordered degree, strength, and digestibility of retrograded gels. Amylose chains, especially short-medium chains with a degree of polymerization (DP) of 100-2500, readily rearrange into long and stable helices during retrogradation, which enhances gel strength and reduces starch digestibility. Similarly, long amylopectin chains (≥ 25 DP) demonstrate amylose-like behavior in their rearrangement propensity. In contrast, short-medium amylopectin chains (6-24 DP) exhibit limited rearrangement capacity due to steric hindrance, resulting in the weakening of gel strength and the reduction of resistant starch content. However, these branches promote intermolecular entanglement to form microcrystals, and their α-1,6-glycosidic bonds are insensitive to digestive enzymes, demonstrating excellent potential in producing slowly digestible starch. This review provides critical theoretical insights for the production and storage of high-quality and slow-digestion starch-based foods.