Starch granule-surface proteins (SGSPs) and gluten proteins can interact to influence dough quality. Despite their pronounced effects, the interaction mechanism remains insufficiently understood. Herein, the binding mechanism between SGSPs and different molecular weight glutenin was explored by experimental methods and single-molecule techniques. Our findings revealed that SGSPs promoted strong binding with both high and low molecular weight glutenin (HMW-GS and LMW-GS). When the ratio of SGSPs and LMW-GS increased to 2:1, the content of disulfide bond increased from 0.03 μmol/L to 0.21 μmol/L while the free sulfhydryl showed the opposite pattern, indicating a tightly packed composite protein structure. A combination of unbiased and steered molecular dynamics simulations further revealed that SGSPs exhibited a higher binding affinity towards LMW-GS in comparison to HMW-GS due to the contributions of solvation and specific interaction energies. This endows the SGSPs-LMW-GS complex with significantly enhanced stability at free state and much higher unbinding force upon stretching, substantially improving the mechanical quality of dough. These findings indicate that SGSPs predominantly affects the interactions between starch and gluten, which will shed light on the dough formation and its properties.