Rice was collected over the entire grain filling period (about 40 days) to explore the multi-structure evolution and gelatinization behavior changes of starch. During the early stage (DAA 6–14), the significant reduction in lamellar repeat distance (10.04 to 9.68 nm) and relative crystallinity (26.6 % to 22.7 %) was due to initial rapid accumulation of amylose (from 9.38 % to 14.05 %) and short amylopectin chains. Meanwhile, the decreased proportion of aggregation structure resulted in a decrease in the gelatinization temperature and a narrowed range of gelatinization temperature also indicated an increase in homogeneity as starch matured. Gelatinization enthalpy was mainly controlled by aggregation structure, which was negatively and positively related to the amylose content and the degree of order respectively. Peak viscosity of starch pasting increased and reached a maximum (924 cP) at DAA-21 due to larger granule size. Amylose and short amylopectin chains with degree of polymerization 6–12 showed positive and negative correlation with short-term retrogradation ability (setback value) respectively. The dynamics of different scale structure during grain filling had varying degrees of impact on gelatinization properties.