In order to investigate the effects of covalent interaction of black kidney bean protein isolate (BKPI) and different concentrations of chlorogenic acid (CA) on the function of the protein, the effects of the covalent interaction of BKPI and different concentrations of CA on protein structure were studied. The relationship between structural change and the functional properties of the complexes was analyzed through dynamic light scattering, fluorescence spectroscopy and Fourier transform infrared (FT-IR) spectroscopy. The results showed that the turbidity and the bonding content of CA in the complexes were increased, and its content of free amino group was decreased with the increase of CA concentration, the covalent interaction made the distribution of droplets in the solution more uniform. The secondary structure of BKPI was changed and the contents of α-helix and unordered decreased, while the contents of β-sheet were increased, and resulting in its conformational change. The decrease in fluorescence intensity with the increase of CA concentration, indicating the unfolding of the protein structure. The addition of CA improved the antioxidant activities and emulsification properties of BKPI. When the concentration of CA was 0.25g/(100mL), the antioxidant activities (168.95μmol/g) and emulsifying properties of BKPI were the best. These results suggested that CA-BKPI complexes could be used as efficient antioxidants and potential emulsifiers in emulsion-food systems.