Ovalbumin (OVA) is widely used to prepare nanocomposites for the delivery of bioactive compounds. During long-term storage of shell eggs, natural OVA is slowly transformed into a more heat-stable form called S-OVA, which can also be obtained artificially through alkali-heat treatment. This study aimed to reveal the effects of alkali-heat and ultrasonic treatment on the structure, stability and polyphenol encapsulation ability of OVA by analyzing the interaction mechanism through molecular docking and multispectral analysis. The results showed that the proteins treated with alkali-heat and ultrasound had higher stability and surface hydrophobicity, reflecting the change in their functional properties. The S-OVA generated by alkali-heat treatment had higher thermal stability and formed softer gels than those generated by ultrasound treatment. The results of infrared spectroscopy and molecular docking indicated that hydrophobic interactions and hydrogen bonds were the main forces stabilizing the formation of catechin-OVA complexes. X-ray diffraction showed that OVA was a good carrier for catechins, which existed in an amorphous state in the hydrophobic core of proteins. Both ultrasound and alkali-heat treatments exposed hydrophobic groups in the protein and significantly enhanced the ability of the protein to bind polyphenols (increased from 15.72 nmol/mg to 44.10 nmol/mg and 43.18 nmol/mg, respectively), resulting in greater antioxidant capacity. This study mainly revealed the binding mode of OVA with polyphenols and explained the reasons for the changes in the functional properties of OVA by revealing the structural changes in proteins under different treatments, providing a basis for the advantages of alkali-heat and ultrasonic treatment of OVA in the food industry.