The aim of this study was to investigate the effect of multi-frequency power ultrasound (sweeping frequency and pulsed ultrasound (SFPU) and sequential dual frequency ultrasound (SDFU)) on the enzymolysis of corn gluten meal (CGM) and on the structures of the major protein fractions (zein, glutelin) of CGM. The results showed that multi-frequency power ultrasound pretreatments improved significantly (P<0.05) the degree of hydrolysis and conversion rate of CGM. The changes in UV-Vis spectra, fluorescence emission spectra, surface hydrophobicity (H0), and the content of SH and SS groups indicated unfolding of zein and glutelin by ultrasound. The circular dichroism analysis showed that both pretreatments decreased α-helix and increased β-sheet of glutelin. The SFPU pretreatment had little impact on the secondary structure of zein, while the SDFU increased the α-helix and decreased the β-sheet remarkably. Scanning electron microscope indicated that both pretreatments destroyed the microstructures of glutelin and CGM, reduced the particle size of zein despite that the SDFU induced aggregation was observed. In conclusion, multi-frequency power ultrasound pretreatment is an efficient method in protein proteolysis due to its sonochemistry effect on the molecular conformation as well as on the microstructure of protein.