The effect of S-configuration transformation on the microstructure of ovalbumin was studied by CD spectra, XRD spectra, ANS fluorescence probe emission spectra and UV absorption spectra. CD spectra was used to examine the changes in the secondary structure of the ovalbumin during S-ovalbumin information process. When the induction time was prolonged, the mutual transformation between α-helix, β-sheet, β-turn and the random coil was observed, and the orderliness of the secondary structure was increased with α-helix decreasing slightly and β-sheet increasing correspondingly. XRD spectra analysis showed that the crystal structure content of the ovalbumin increased with prolonging the induction time and the largest data was observed at 72 h, indicating that the orderliness of the secondary structure was increased. The results were similar to CD spectra analysis. The ANS fluorescence probe emission spectra analysis demonstrated that S-configuration transformation induced an increase in surface hydrophobicity with prolonging the induction time, and the largest data was also observed at 72 h. In addition, UV absorption spectra analysis indicated that S-configuration transformation resulted in a decrease in the UV-absorption maximum value with prolonging the induction time, indicating that the aromatic amino acid was buried in the molecular interior. The results indicated that the changes in the microstructure of ovalbumin were relevant to S-configuration transformation.