The genotype of rice variety is important factor that affect grain quality during storage. In this study, japonica, indica, and indica-japonica hybrid rice were selected to reveal the changes in amylase activities, starch fine structure, and physicochemical properties after one year of storage. Amylase activities decreased after storage and starch molecules were degraded, which, respectively, decreased and increased the content of the amylopectin long chains (DP 37+) and amylose. Changes in the starch fine structure resulted in lower swelling factors and a higher gelatinization temperature. Compared with japonica and indica-japonica hybrid rice, indica rice had a more stable starch fine structure and physicochemical properties after storage. The information obtained from this study provides a better understanding of the changes that occur in starch at the molecular level during storage and will provide insight into the breeding of storable rice varieties.