For solving the problem of feeding the increasing world population, the physicochemical, cooking, textural, pasting, microstructural, and thermal properties of two early indica rice varieties (newly harvested SRN variety and IP46 variety with one-year in-bin storage) were analysed over 12 months of storage at 15°C and 30°C, respectively. A General Linear Model Univariate (GLMU) analysis was adopted to show the significant effects of three factors (variety, storage temperature, and time). Compared with 15°C storage, 30°C storage resulted in higher free fatty acid (FFA) content, amylose content, conductivity, kernel broken index, chalky kernel percent, and chalkiness degree and a reduced taste value. The cooking test showed that 30°C storage increased the cooking time and the hardness of cooked rice but decreased the gruel solid loss and the adhesiveness and resilience of cooked rice. Compared with 15°C storage, 30°C storage increased the pasting temperature and peak, breakdown, and setback viscosities of the two early indica rice varieties. Moreover, there was an increase in the peak temperature of gelatinization but no change in starch ageing. Infrared spectroscopy analysis confirmed that, in contrast with 15°C storage, 30°C storage increased the crystallinity of starch, the interaction between protein and starch, and the β-sheet percent in the early indica rice. Microstructure analysis showed that SRN raw rice exhibited a consistent polygonal shape of starch granules after 12 months of storage at 30°C, but the edges of the chalky portion of the starch granules were not obvious in IP46 rice. It can be concluded that 30°C storage can maintain the taste value, paste aging, and cooked rice texture of early indica rice after two years of storage, despite blurring of the edges of the chalky portion of starch granules.