In this study, the impact of different thermal methods (cooking and steaming treatment) on the structural variations of native and heat-moisture treated (HMT) rice starches and their effect on starch digestibility were investigated. As expected, HMT induced the disruption for starch semi-crystalline lamellae, crystallites, and helical structures. After thermal processing, varied destructions were obtained for lamellar, crystalline and helical structures of native and HMT-treated rice starches, especially under cooking treatment. And these structural alterations may improve the RDS fraction of rice starches and decrease their SDS and RS fractions. Particularly, steamed starches displayed higher enzyme resistance than their cooked counterpart, which may be attributed to the limited destruction of starch hierarchical structure during steaming process. And the aboved transformations demonstrated that water accessibility during thermal processing played a key role in starch structure and digestibility. Furthermore, HMT-treated starch still remained more crystallites and helices after thermal processing, thus resulting in slower digestibility. This work may be beneficial for encouraging the utilization of HMT-treated starch in food processing and obtaining gelatinized starch-foods with special nutritional functions.