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We analyzed the relationship between the nanometer-scale structure of amylopectin and physicochemical properties such as thermal properties of starch granules and higher-order internal structure of starch granules evaluated by using synchrotron radiation X-ray scattering and scanning electron microscopy. In this study, a line of allelic mutants of rice lacking in starch branching enzyme IIb (BEIIb) activity in their endosperm were used as starch sources. The crystal lattice changed from A-type to C- and B-type. The nanoscale cluster size, and higher-order structures of the starch granules varied among mutant lines. The thermal gelatinization properties of the rice-derived starch samples, as well as the dependence of this process on their crystal structure, were evaluated using differential scanning calorimetry and synchrotron X-ray scattering. After gelatinization, several nm-scaled density fluctuations owing to the formation of gel balls were observed. These fluctuations of all starch samples correlated with the cluster size decreased with the temperature.