The purpose of this study was to investigate the effects of different structures of corn starch (high amylose corn starch, normal corn starch, and waxy corn starch) on the processing quality of dough. The rheological properties, thermal properties, microstructure and physicochemical properties of gluten proteins in the simulated dough of corn starch were determined. The results showed that the viscoelasticity of the high-amylose corn starch mock dough was significantly higher than that of the normal/waxy cornstarch mock dough, which was attributed to its non-gelatinization and highly filling characteristics. Waxy corn starch significantly inhibited the thermal aggregation of gluten proteins through competitive water absorption, resulting in a relatively loose structure of the dough after heat treatment. The results of molecular weight distribution and intermolecular interactions also confirmed that waxy corn starch mainly inhibited the formation of high molecular weight gluten proteins by hindering the crosslinking of disulfide bonds, leading to the transition of gluten proteins from a rigid α-helix to a disordered β-turn structure. This study helps to gain a deeper understanding of the interaction mechanism between starch and gluten proteins, and provides a reference for improving the processing quality of flour products by regulating the structural characteristics of starch.