Ultrasound was applied to facilitate starch-protein separation in ultrasound-assisted laboratory-scale corn wet-milling. Changes to the molecular structure of glutelin and zein in the corn gluten meal treated by sonication were investigated to explore their roles in the release of starch. Sonication (130 to 200 W, 15 to 60 min) was found to cause the unfolding of the glutelin, as demonstrated in the decrease in disulphide bonds (SS) content, α-helix and β-turn, and the increase in free sulfhydryl (SH) content, β-sheet and random coil. Furthermore, the solubility, surface hydrophobicity and fluorescence intensity of the glutelin (200 W/60 min) increased by 141.75, 109.18 and 186.01%, respectively, while its denaturation temperature (T d ) and endothermic enthalpy (ΔH) decreased by 7.43 and 21.51%. Compared with control zein, after 60 min sonication at 200 W, the SS content and α-helix of the zein were found to have decreased by 20.68 and 19.14%, and its SH and random coil increased by 26.61 and 18.21%. Accordingly, the solubility, surface hydrophobicity and fluorescence intensity of zein increased by 54.03, 6.85 and 84.62%, and its T d and ΔH decreased by 5.76 and 4.19%. It was, thus, concluded that glutelin is more sensitive than zein to sonication and that the unfolding of glutelin is critical to the release of starch granules.