Seeking safe and environmentally friendly natural immunomodulators is a pressing requirement of humanity. This study investigated the differential binding characteristics of two polar polyphenols (PP), namely epicatechin (EC) and chlorogenic acid (CA), to ovotransferrin (OVT), and explored the relationship between structural transformations and immunomodulatory activity of OVT-PP complexes. Results showed that CA exhibited a stronger affinity for OVT than EC, mainly driven by hydrogen bonds and van der Waals forces. Complexation-induced conformational variations in OVT, including static fluorescence quenching, increased microenvironment polarity surrounding tryptophan and tyrosine residues, and the transition from disordered α-helix to stable β-sheet. Furthermore, the structural conformation transformation of OVT-PP complexes facilitated the enhancement of immunomodulatory activity, with the OVT-CA (10:2) complex demonstrating the best immunomodulatory activity. Principal component analysis (PCA) and Pearson correlation analysis revealed the immunomodulatory activities of the OVT-PP complexes were influenced by surface hydrophobicity (negatively correlated), β-sheet percentage and polyphenol binding constants. It could be inferred that PP complexation increased the surface polarity of OVT, consequently enhancing its immunomodulatory activity by promoting cell membrane affinity and antigen recognition. This study provides valuable guidance for effectively utilizing polyphenol-protein complexes in enhancing immunomodulatory activities.