Supplemental irrigation (SI) is an important strategy to improve the water-use efficiency (WUE) of crops without compromising the yield. However, such strategy can influence the starch and grain quality. Hence, the effects of SI on winter wheat starch structure and functionality were studied on ridge-furrow (RF) and flat tillage (FT) treated fields. Flat irrigation was set as control. RF + SI significantly increased the grain yield throughout the study period (2016–2018). SI decreased the amylose content and the content of amylopectin chains with DP 13–24 but increased the proportions of amylopectin chains with DP 6–12 and 25–36. The starch granule relative crystallinity decreased, and more B-type granules were produced by SI treatment. SI significantly increased the resistant starch content in both raw and cooked starch systems. Flat tillage enhanced the effect of SI on granule specific surface area (SSA) and viscosity, which increased starch paste viscosity, while SI + RF showed the opposite effects. Our study demonstrates important combined effects of SI and tillage on wheat starch quality.