Extremely high temperature (HT) is a critical factor limiting maize yield and quality, particularly during the flowering and early grain-filling stages. The study aimed to explore the differential effects of HT during flowering (T1), early grain-filling (T2), and both stages (T3) on the physicochemical properties of starch in normal and waxy maize. For waxy maize, T2 increased the retrogradation percentage (%R) and the content of rapidly digestible starch, whereas T1 had no significant effect in this regard. T3 increased the starch granule size, relative crystallinity (RC), and pasting characteristics, but decreased the starch content. In contrast, for normal maize, T1 enhanced kernel weight, whereas T2 increased RC and %R significantly without affecting the pasting properties. Moreover, T1 altered gelatinization characteristics by modifying starch morphology and granule size, whereas T2 further impacted starch structure, thereby affecting quality and digestion properties. Overall, waxy maize exhibited greater sensitivity to HT than normal maize.