Spray drying is an important processing of producing modificatied yolk powder (MEYP). To investigate the correlation between the secondary structure and emulsifying property of MEYP made at different spray-drying-temperatures, Fourier transform infrared spectroscopy (FTIR) was applied in the present study. The result indicated that emulsifiability and the percentage of α-helix were both significantly increased firstly and then remarkably decreased with rising of spray-drying-temperature, and the emulsifying property of MEYP was relative to the percentage of α-helix. After heat-treating, the percentage of α-helix was significantly decreased and the percentage of β-sheet was remarkably increased, however, the total percentage of the two structures was maintained. The stable total percentage of α-helix and β-sheet would be a good explanation for the great heat stability of emulsion presented in the MEYP made at different spray-drying temperature.