Abstract The aim of the present study was to investigate the alterations of the physiological properties associated with the ultrastructure changes of rice seed after drying at different temperatures. The drying process was accomplished at 30, 45, 60, 75 and 90°C and at 29.3%, 13.0%, 6.4%, 3.2%, and 1.8% relative humidity, respectively. As a result, the germination percentage of the rice seeds was reduced as the increasing of the drying temperature and the highest value of vigor index was recorded at 45°C due to the dormancy breakage. There were no changes in the color of the raw rice seed dried at different temperatures; however, the yellowness of the brown rice and the electrical conductivity increased with the increasing drying temperature. The starch granules of the rice endosperm dried at 45°C were wrinkled and wilted and this damage occurred with high intensity after drying at temperatures above 60°C. The structure of the starch granules eventually became rupture when the drying temperature reached to 90°C. The cells of the rice embryo presented a contraction of their volumes drying at temperatures above 45°C due to the degradation of the middle lamella. The form of the oil drops was also altered after drying. At temperature above 75°C, the drops broke up and coalesced. It was concluded that the physiological quality of rice seed was closely associated with the alterations of cell structure during drying process.