High-amylose wheat, developed using non-transgenic methods, has gained considerable attention due to its high intrinsic resistant starch, which provides notable health benefits. However, there is still limited understanding of high-amylose wheat from a protein perspective. In this study, proteins from a wild-type (durum wheat AM01, 24 % amylose content, bread wheat RS01, 23 % amylose content) and its high-amylose counterpart (durum wheat AM02, 59% amylose content, bread wheat RS126, 62% amylose content) were comparatively evaluated across multiple structural levels. Although the crude protein content in high-amylose wheat increased by 4-5%, the SDS-PAGE profile of soluble protein remained similar to that of wild-type wheat. However, Fourier-transform infrared (FTIR) analysis revealed that high-amylose wheat exhibited a higher proportion of beta-sheets and a lower proportion of alpha-helices in its secondary protein structure. This structural shift suggests that increased amylose content may alter the protein matrix, enhancing interactions between protein molecules while reducing the ability to form hydrogen bonds. The protein molecular size distribution was altered in durum wheat but remained consistent in bread wheat. Additionally, high-amylose wheat demonstrated an enhanced water-binding capacity. The dough made from high-amylose wheat exhibited improved elasticity and resistance to deformation. These findings provide new insights into how high-amylose wheat protein structure influences dough properties, offering opportunities for optimizing wheat-based ingredients and processing.