Measuring the germination index of corn, and gelatinization index, thermodynamic properties, long-range structure, short-range structure and particle morphology of corn starch, the study aimed to investigate the effects of different microwave (MW) treatment on the structural and functional properties of germinated corn starch. The results indicated that after appropriate MW treatment, the germination indices (germination rate, germination potential, sprout length and sprout weight) of germinated corn starch were improved after 7 days of germination. In addition, MW treatment also affected the structure of germinated corn starch. MW treatment could reduce the relative crystallinity of starch, but did not change the crystal type and the peak position of each absorption peak in Fourier transform infrared spectra. In addition, rapid visco-analysis and differential scanning calorimetry results showed, respectively, that MW treatment decreased the peak viscosity of germinated corn starch and increased the gelatinization temperature. Finally, MW treatment made the starch surface become rough, destroyed the starch particle structure and produced random cracks and voids. Overall, the present study proves that appropriate MW treatment is an effective measure for the modification of germinated corn starch, and provides a theoretical basis for the application of MW technology in germinated corn products. © 2024 Society of Chemical Industry.