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BACKGROUND The composition of glutenin protein significantly affects protein-starch interactions and starch digestion characteristics in wheat dough matrices. To elucidate the effects of high molecular weight glutenin subunits at the Glu-B1 locus on dough processing quality, the detailed structural changes of protein, starch, and their complexes were compared in Mixolab dough samples of two near isogenic lines 7+8 and 7+9. RESULTS The results showed that the degree of protein aggregation increased continuously during dough processing, as did the destruction and rearrangement of the gluten network. Compared to 7+8, the stronger and more stable protein network formed in 7+9 dough induced intensive interactions between protein and starch, primarily through hydrogen bonds and isomeric glycosidic bonds. In 7+9 dough, the more compact and extensive protein-starch network significantly inhibited starch gelatinization during dough pasting, while during the dough cooling stage (from C4 (82.8 °C) to C5 (52.8 °C)), more protein-starch complexes composed of monomeric proteins and short-chain starch were generated, which remarkably inhibited starch retrogradation. All protein-starch interactions in the 7+9 dough improved the starch digestion resistance, as reflected by the high content of resistant starch. CONCLUSION The more extensive and intensive protein-starch interactions in the 7+9 dough inhibited the gelatinization and enzymatic hydrolysis of starch, thereby producing more SDS and RS. These findings demonstrate the feasibility of optimizing the texture and digestibility of wheat-based food products by regulating the behavior and interactions of proteins and starch during dough processing. This article is protected by copyright. All rights reserved.