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This work investigated the effects of water-deficit and high-nitrogen (N) treatments on wheat resistant starch (RS) formation, molecular structure, and physicochemical properties. The results of consecutive 2-year field experiments revealed that water deficit significantly reduced starch granule number and diameter, amylose, RS content, RS particle size distribution, and physicochemical properties, including peak and trough viscosities, oil absorption capacity, and freeze-thaw stability. Water deficit also altered the long- and short-r