Abstract A series of diluted and concentrated wheat gluten solutions were used in this experiment to carry out deamidation under moist heat. During the moist-heat-induced denaturation, the effect of molecular structure and aggregation state of wheat gluten on the degree of deamidation was analyzed. The results showed that the degree of deamidation, degree of hydrolysis, and zeta potential significantly decreased with increasing aggregation of native wheat gluten. Additionally, both degree of deamidation and hydrolysis had a good linear relationship with the changes in the aggregation state of wheat gluten. The intermolecular force of wheat gluten significantly increased with increasing aggregation of native wheat gluten, and the red shift became smaller. The intermolecular noncovalent bonds, including hydrogen bonding and hydrophobic interaction, were the main molecular forces for the aggregated wheat gluten; disulfide bonds had a minimal effect. These results demonstrated that the aggregation state of native wheat gluten is closely related to the rate of wheat gluten deamidation via moist heat treatment using food-grade organic acid. The aggregation state of native wheat gluten is the most important factor for the unfolding degree of protein molecules and aggregation trends of wheat gluten.