Given the rising global prevalence of diabetes, the glycemic index of rice as a staple food constitutes a significant dietary risk factor. To elucidate how chemical composition and multi-scale structure regulate starch digestibility in rice, five typical rice varieties with varied resistant starch contents were systematically characterized with respect to their basic components, amylopectin chain-length distribution, crystalline properties, pasting and rheological characteristics, and gel strength. Combined with microstructural observation and starch digestion kinetics modeling, the composition of digestive fractions and estimated glycemic index (eGI) were determined. The results revealed that the japonica rice variety R1 exhibited the lowest eGI (47.73), whose resistance was attributed to the synergistic effects of multi-scale architecture, wherein high protein and lipid contents formed a dense barrier network, and amylose-lipid complexes generated V-type crystallites (24.7%). Amylose further promoted retrogradation, yielding the highest retrogradation viscosity and gel strength that constrained enzymatic hydrolysis efficiency. Correlation analysis demonstrated that both protein content and gelatinization temperature were significantly positively correlated with resistant starch content, whereas amylose primarily facilitated resistant starch formation by suppressing the digestion rate constant of rapidly digestible fractions. In conclusion, protein network barriers, amylose-driven retrogradation, and elevated gelatinization temperature are critical factors regulating rice starch digestion rate. These findings provide a theoretical basis for breeding and precision processing of low-GI rice varieties.