This study investigated the influence of inulins with different molecular weights (Mw) and added concentrations on the structure and thermal stability of gliadin and glutenin gels. All inulins reduced hydrophobicity index (H0) and hindered disulfide bond (S–S) formation of both glutenin and gliadin. The H0 of glutenin reduced by 72.6%, 64.8% and 77.1% after the addition of 400 g/kg low, middle and high molecular weight inulins (L-, M-, and H-inulin, respectively), whereas the H0 of gliadin decreased by 11.7%, 31.9% and 48.6%. Furthermore, inulin increased random coils and decreased α-helix and β-sheet prevalence for gliadin, while it increased α-helix and β-turn prevalence and decreased β-sheets and random coils for glutenin. Inulin also triggered S–S configuration of these two proteins to vary from g-g-g to t-g-g or t-g-t. H-inulin deepened gel electrophoresis bands of the 30–35 kDa gliadin molecules, and all inulins reduced band strength for the 30–35 kDa glutenin subunits. Inulin limited interactions between glutenin/gliadin and water, resulting in more fragile and open network structure. Moreover, the thermal stability of heat-induced inulin-gliadin gel was higher than that of inulin-glutenin gel. The impact of inulin on glutenin was stronger than on gliadin, and the effect was Mw-dependent (H-inulin > M-inulin > L-inulin).