In order to clarify the effects of alkaline covalent binding, enzymatic covalent binding and free radical covalent binding of soybean lipophilic protein (LP) to chlorogenic acid (CA) on the conformational and functional properties of proteins and the mechanism of binding. Accordingly, this study comprehensively employed particle size and Zeta potential analysis, electrophoresis, multispectral techniques, differential scanning calorimetry, rheology, scanning electron microscopy, and antioxidant activity assays to characterize the molecular weight, secondary and tertiary structures, thermal stability, rheological properties, and antioxidant capacity of the complexes under different preparation conditions. The results demonstrated that the polyphenol binding rate of LP increased based on free radical, base and enzyme conditions, and particle size and the absolute values of Zeta potential were higher than those of LP. The content of free amino group and sulfhydryl group decreased, but the content of disulfide bond increased, with the most significant changes observed in the enzymatic complexes. The introduction of CA shifted the electrophoretic bands of LP upward, and the subunits in the LP molecule were denatured into small molecular subunits, with progressively more significant denaturation of the free radical complexes, the alkaline complexes, and the enzymatic complexes. The free radical complexes, enzymatic complexes and alkaline complexes had sequentially increased ionic bonding content and sequentially decreased hydrophobic force compared to LP. The results of circular dichroism and Fourier infrared spectroscopy indicated that CA was successfully complexed with LP, and the two were mainly connected through C-N/C-S bonds, with an elevated content of random coils and a reduced content of β-sheets and β-turns in the complexes, and the most significant changes in the secondary structure of the alkali complexes. The intrinsic fluorescence results indicated that the enzymatic complex exhibited the strongest fluorescence quenching effect, followed by the alkali complex. The surface hydrophobicity of the complexes decreased, and that of the alkaline complexes was the lowest. The thermal stability and rheological properties of the complexes, especially the alkaline complexes, were enhanced. The incorporation of CA resulted in more protrusions and pores on the surface of LP, and the microscopic morphology of the free radical complexes, the enzyme complexes, and the alkaline complexes became more homogeneous and dense. The antioxidant capacity of the LP-CA covalent complexes increased after digestion. The free radical complexes possessed the strongest antioxidant capacity, while the enzymatic complexes had the weakest antioxidant capacity. This study can provide a theoretical basis for the application of LP-CA complexes as functional ingredients and the development of CA-containing soy protein products.