The digestion results showed that a short-term (1 d) refrigeration allowed a significant increase in the content of slowly digestible starch by about 40%. As inspected by combined techniques such as small angle X-ray scattering, the short-term storage reduced the micron scale pore size, and allowed starch and protein chain reassembly into relatively flawed structures such as short-range orders, long-range starch crystallites and nonperiodic nanostructure; these structural changes resulted in the formation of structural domains with slowly digestible features. However, further prolonging the storage time strengthened the perfection of the reassembled structures, thus transforming partial slowly digestible fractions and negligibly influencing other digestion features. The present results could facilitate the production of high-quality cold chain cooked rice with demanded starch digestibility.