Red kidney bean cells were isolated under atmospheric hydrothermal treatment with varying temperatures and incubation periods to elucidate how these conditions affect the structure and in vitro digestibility of starch in bean cells. A comprehensive analysis was conducted using a combination of morphological, X-ray diffraction, thermal property, and in vitro simulated digestion analyses. Results indicated that red kidney bean cells isolated at 80–100 ℃ maintained their morphological integrity. The starch within these cells was not fully gelatinized, and the crystal structure was partially disrupted, retaining a degree of relative crystallinity (12.97%~16.54%). Compared to processing duration, temperature imposed a more significant impact on the starch crystal structure. With an increase in heat treatment temperature (80~100 ℃) and incubation period (25~45 min), increases were observed in the fluorescence intensity of the intracellular dextran isothiocyanate probe, in vitro digestion rate of starch (0.004 6~0.006 6 min−1), and degree of digestion (56.25%~69.25%). Between 80 and 90 ℃, cell wall permeability was the major influencing factor of starch digestibility; both cell wall permeability and starch crystallinity simultaneously affected starch digestibility in cells when the temperature rose to 100 ℃. Therefore, by modulating the temperature and duration of atmospheric hydrothermal treatment, the digestive properties of starch contained in red kidney bean cells can effectively be regulated. This study identified changes in the nutritional characteristics of starch components in legumes during thermal processing, providing theoretical guidance for the development of legume-based functional foods.