In this study, hierarchical structural and characteristic changes of starches isolated from repeated freezing-thawing (FT) frozen dough were evaluated to understand the causal relations among intrinsic structures and physicochemical characteristics. The surface of FT-treated starch granules displayed pores and cracks, and more severe rupture was obtained as the increase of freezing-thawing cycles. Furthermore, the lamellar structure, crystalline and ordered molecular structure (i.e., short-range ordered molecular and helical structures) of starch were also destructed after FT. And these structural amorphization facilitated the interactions between water molecules and starch molecular chains, the leaching of starch molecules, the entanglements and interactions between amylose and amylopectin, eventually elevating the swelling power, solubility and characteristic viscosity of starch. Also, FT treatment led to an increase in storage modulus (G’) and a decrease in loss tangent (tan δ), which indicated the formation of strong gel network structure.