•Physicochemical and structural modification of starch depended on its type and annealing method.•Annealing could reduce the molecular weight of wheat starch.•Repeated annealing exhibited its superiority in improving crystal order of normal wheat starch.•Repeated annealing was more effective in increasing molecule interaction of starch. Effects of repeated annealing treatments (8 cycles, 12 h each) or continuous annealing treatments (12–96 h) at 50 °C on structural, physicochemical, and digestive properties of normal and waxy wheat starches were investigated. Wheat starches retained the original crystalline structure of A-type after annealing. Annealing treatments increased crystallinity, short chain of amylopectin, viscosity, and gelatinization temperatures of starch. However, molecular weight, long chain of amylopectin, solubility, and swelling power of starch decreased after annealing. Additionally, annealing reduced the in vitro digestibility of wheat starches. The changes in properties of starch varied depending on starch type, normal or waxy, and annealing methods, repeated or continuous. The repeated annealing was found to be more effective in modification of normal wheat starch properties. However, continuous annealing efficiently modified properties of the waxy wheat starch. The obtained results may help in choosing appropriate applications of annealed wheat starches in the food industry.