Starch is the main composition of frozen dough. How the freezing rate of frozen dough affected multi-scale structures and functionalities of starch in the frozen dough and the underlying mechanism are not systematically discussed yet. Both rapid and slow freezing treatment (0.20–1.50 ℃/min) increased the content of amylose, helical structures, crystalline structures, and short-range ordered structures and the thickness of crystalline lamellae and semi-crystalline lamellae, and thus increased swelling power, solubility, peak viscosity, breakdown viscosity, final viscosity, and setback viscosity of starch during heating. A slow freezing treatment (0.20 ℃/min) contributed to the formation of large ice crystals, and in turn, resulted in great changes in starch structures and functionalities. The corrosion of starch granules and the leach of amylose and small amylopectin during the thawing of ice crystals may be responsible for the changes in structures, swelling power, solubility, and pasting properties of starch in the frozen dough.