In this study, Denghai-685 and Xianyu-335, two major corn cultivars cultivated in East China, underwent hot air drying with different initial moisture contents (20, 25, and 30%) and drying temperatures (60, 90, and 120 °C). The study analyzed the dried corn kernels' starch structure and physicochemical characteristics. Hot-air drying altered the starch shape, transforming it from spherical to polyhedra. This process also reduces the amount of amylose in corn compared to naturally dried samples. Interestingly, higher drying temperatures (90 and 120 °C) increased gelatinization temperature but decreased other gelatinization parameters for both cultivars. The transparency of starch pastes from the two cultivars was improved, but the retrogradation was weakened. The onset, peak, and conclusion temperatures of starches increased as the drying temperature rose, while the gelatinization enthalpy decreased. Hot-air drying increased the relative crystallinity of starches of the two cultivars, peaking at 60 °C. The changes in values of R_1047cm⁻¹_/1022cm⁻¹ and R_995cm⁻¹_/1022cm⁻¹ deduced from infrared spectroscopy suggested that hot-air drying promoted a more ordered crystalline structure of starches from the two cultivars. These findings suggested that the physicochemical and structural characteristics of starches from the two cultivars were significantly influenced by the interaction of initial moisture content and heating temperatures.