To improve the eating quality and stability of whole wheat steamed buns, the quality of steamed buns with different content of whole wheat flour (WWF) and the behavior of gluten protein aggregation were investigated in the process of proofing. The results revealed that the hardness and porosity of whole wheat steamed buns gradually increased during the proofing. The hardness reached 903.33 N at the lowest level and the content of free SH was 4.26 μmol/mL at about 10 min after the proofing. The intermolecular electrostatic repulsion increased and the gluten system tended to be stable; The elasticity of 50% whole wheat flour steamed buns can reach 0.93 at most. The WWF is beneficial for maintaining intermolecular hydrogen bonding and hydrophobic interactions, and enhancing the thermal stability of gluten proteins. AFM results also showed that the gluten protein aggregate height of 50% whole wheat steamed buns could reach 26 nm at 10 min of proofing, and the integrity of the gluten network was high. The excessive WWF inhibited the stretching of gluten proteins during the proofing, which led to the increase of hardness of steamed buns and the destruction of internal structure. The increase in the hardness of steamed buns caused by excessive proofing is mainly due to the abnormal aggregation of gluten. It provides reference for whole wheat steamed buns processing.