The effects of water deficit after pollination on the physicochemical properties of waxy maize starch were clarified, using Suyunuo5 and Yunuo7 as test materials. Pot experiments were conducted in 2012 and 2013; a pool trial was performed in 2014. Results indicated that the starch granule size was decreased by water deficit in both pot and pool experiments. Furthermore, the water deficit reduced the starch crystallinity and peak intensities at different reflection angles. The reduced iodine binding capacity under drought condition indicated that the proportion of long chains in amylopectin was decreased by water deficit. Swelling power was only decreased by drought under pool condition. The structural changes in starch decreased the peak and breakdown viscosities, but increased the retrogradation percentage. The maximum absorption wavelength, blue value, gelatinization enthalpy, pasting and gelatinization temperatures of starch were not affected by the water deficit. Therefore, drought during grain filling deteriorated the pasting viscosities and increased the tendency of retrogradation by reducing the starch granule size, proportion of long-chains in amylopectin, swelling power, and crystallinity.