In this study, Raman spectroscopy and circular dichroism spectra of soy protein isolate solutions subjected to different homogenization conditions were acquired for investigations on the effects of low pressure homogenization on the structure of soy protein isolate. The results showed that the secondary structure of soybean protein isolate basically remained unchanged when the homogenization pressure was low (0~8 MPa). When the homogeneous pressure was 10~30 MPa, the α-helical and random coil structures increased significantly, β-sheet decreased significantly. Thetryptophan and tyrosine residues gradually changed from “buried state” to “exposed state”, and the protein molecule exhibited depolymerization behavior; Over the course of the increase of homogenization pressure to 40 MPa, the ratio of tyrosine - Fermi resonance line I850/I830 decreased slightly, and the tyrosine residue changed from “exposed state” to “buried state”, indicating that protein aggregates were produced, and low pressure homogenizatio did not significantly alter the configuration of disulfide bonds. In summary, the secondary structure and tertiary structure of protein molecules can be characterized by Raman spectroscopy, and obtained results revealed that low-pressure homogenization induced depolymerization and then polymerization of soy protein isolate. These results were confirmed by circular dichroism.