This study aimed to examine the effect of translutaminase (TGase) cross-linking on the molecular structure of soybean protein isolate (SPI). The structural changes of SPI before and after cross linking were analyzed by differential scanning calorimetry (DSC), scanning electron microscopy, X-ray, infrared spectroscopy and circular dichroism spectroscopy. The results showed that after being cross-linked, the surface hydrophobicity of SPI increased, and the content of free amino groups reduced. The structure and microcrystal structure changed from spherical to concave, with the polypeptide chains stretched adequately, the spatial structure changed and the crystallinity decreased; the β-fold content increased, the structure becoming more ordered, while the random coil content decreased. Finally, we found that the content of essential amino acids increased by 5.5% and the content of hydrophobic amino acids by 14.5%, indicating that the nutritional value and surface hydrophobicity of SPI was improved after cross linking, as analyzed by an amino acid automatic analyzer. © 2019, China Food Publishing Company. All right reserved.