Waxy maize starch serves as a pivotal component in global food processing and industrial applications, while high temperature (HT) during the grain-filling stage seriously affects its quality. Salicylic acid (SA) has been recognized for its role in enhancing plant heat resistance. Nonetheless, its regulatory effect on the quality of waxy maize starch under HT conditions remains unclear. In this study, two waxy maize varieties, JKN2000 (heat-tolerant) and SYN5 (heat-sensitive) were treated with SA after pollination and then subjected to HT during the grain-filling stage to explore the effect of SA on grain yield and starch quality. The results indicate that exogenous SA under HT treatment led to an increase in kernel weight and starch content in both varieties. Moreover, SA reduced the HT-induced holes on the surfaces of starch granules, enlarged the starch granule size, elevated the amylopectin branching degree, and reduced amylopectin average chain length. Consequently, improvements of pasting viscosity and the decrease of retrogradation percentage of starch were observed with SA under HT. Exogenous SA reduced HT-induced rapidly digestible starch content in SYN5, but had no significant effect on that in JKN2000. In summary, SA pretreatment effectively alleviated the detrimental effects of HT on starch pasting and thermal properties of waxy maize.