The conjugation of protein and chlorogenic acid was expected to change protein structure and improve protein functional properties. The study investigated the effect of covalent interactions of soy protein isolate (SPI) and chlorogenic acid (CA) at different concentrations (20, 40, 60, 80, 100 mu mol/g protein) on the interface-related functions and antioxidant activities. The results showed that the conjugation rate was directly proportional to the CA concentration. The results of SDS-PAGE analysis revealed that covalent complexes were formed. The intrinsic fluorescence spectroscopy and ultraviolet spectroscopy indicated that CA tended to unfold the structure of SPI. Correspondingly, the flexibility was greatly enhanced by 183.06%, and a significant decrease (26.06%) in the surface hydrophobicity was caused. In addition, the DPPH and ABTS radical scavenging activities constantly increased by 10.87% and 33.08 mu mol Trolox Equivalent (TE)/g protein with CA of 100 mu mol/g protein. However, the solubility, emulsifying stability and foaming properties increased first and then decreased with the increase of CA concentration. They all reached the maximum when CA was 80 mu mol/g protein, respectively, 47.77 +/- 0.15%, 39.55 +/- 1.27 min, and 3155.76 +/- 52.02%. And the particle size was the smallest at this time, particles smaller than 10 nm had the largest volume fraction. In summary, SPI had the greatest improvement in the interface-related functional properties and excellent antioxidant activities with CA of 80 mu mol/g protein. This work elucidates that SPI-CA covalent conjugates can be used as a new food ingredient in emulsion food systems to improve food quality.