Maize starch is an important source of industrial starch in the world, and its production is seriously affected by water deficit. Waxy maize starch is composed of nearly pure amylopectin, which endows with its high economic value. The effects of mild, moderate, and severe drought stresses during grain filling on the structural and functional properties of waxy maize starch were evaluated using two hybrids as materials. In general, the starch granule size enlarged, the branching degree decreased, and amylopectin chain length and relative crystallinity increased when both hybrids suffered post‐silking water deficit in 2 years. Meanwhile, the influence of drought degree on these starch structures depended on the hybrid and year. Peak, breakdown, and setback viscosities gradually decreased with the severity of water shortage, and trough and final viscosities were the lowest under severe drought conditions. Gelatinization enthalpy gradually decreased with the water supply decrease, and gelatinization temperatures showed an opposite trend and were the highest during severe drought. Correlation analysis indicated that the decrease in pasting viscosities and gelatinization enthalpy and the increase in gelatinization peak temperature may be due to the high proportion of low‐molecular‐weight amylopectin, low proportion of DP 25–36 chains and large granule size of starch. Furthermore, drought stress was easily destroyed the starch structure of JKN2000 and the pasting viscosities and gelatinization enthalpy of SYN5. In conclusion, water deficit during grain filling affected the structural and physicochemical properties of waxy maize starch. The lowest pasting viscosities and gelatinization enthalpy and the highest gelatinization temperatures were observed when these plants suffered severe water shortage during grain filling.