The effects of pulsed electric field (PEF) under 50 kV·cm-1 as well as heat treatments on the secondary structure of soy protein isolate (SPI) were investigated by Fourier transform infrared (FTIR) method in the present paper. A set of self-designed and made PEF equipment was used. It was demonstrated from the FTIR spectra that the PEF treatment under 50 kV·cm-1 had induced the increase in hydrogen bonds amidst in the intermolecule and intramolecule of SPI, and the increase in C—O—O bonds stretch vibration and the PO or P—O—C stretch vibration, which is positive relative to the increase in the time of PEF treatment. It was shown that after PEF treatment, the ratio of α-helix and β-sheet structure in SPI was decreased by 5.9% and 0.7%, respectively. On the other hand, the ratio of β-turn and side chain vibration structure was obviously increased by 7.5% and 9.6% at the treatment time of 1 600 μs, respectively. Comparatively the effect of heat treatments with 90 ℃ for 30 min on the C—O—O bonds stretch vibration and the PO or P—O—C stretch vibration is more evident, but the effect of which on the secondary structure of SPI is less. So it is concluded that the effect mechanism of PEF and HT on SPI structure is significantly different.