BACKGROUND: Drought stress (DS) is the main abiotic stress that maize suffers during its whole growth period, and maize is also sensitive to DS. It had been demonstrated that DS could improve the quality of normal maize starch. However, waxy maize, which has special properties, has not been explored in depth, which limits the breeding and cultivation of waxy maize varieties and the application of waxy maize starch. Therefore, in this study, we investigated the effects of DS on the biosynthesis, structure, and functionality of waxy maize starch. RESULTS: The results showed that DS decreased the expression level of SSIIb, SSIIIa, GBSSIIa, SBEI, SBEIIb, ISAII, and PUL, but increased the expression level of SSI and SBEIIa. DS did not change the average chain length of amylopectin, while increased the relative content of fa chains (RC_fa) and decreased the RC_fb1 and RC_fb3. Furthermore, DS decreased the amylose content, amorphous lamellar distance d_a, semi-crystalline repeat distance, and average particle size, whereas it increased the relative crystallinity, crystalline distance d_c, the content of rapidly digested starch in the uncooked system and resistant starch content in both the uncooked and cooked system. Conclusions: For waxy maize, DS could raise the relative expression level of SSI and SBEIIa, thus increasing RC_fa. The larger number of RC_fa could create steric hindrance, which can lead to producing more resistant starch in waxy maize starch.