The interaction between proteins and polyphenols helps mitigate the decrease in protein digestibility caused by oxidation. This study aimed to examine the effects of structurally varied polyphenols─propyl gallate (PG), gallic acid (GA), protocatechuic acid (PCA), and rosemary extracts (RE)─on the degree of oxidation and digestibility of eel myofibrillar protein (MP) under oxidative stress, clarifying their binding modes and mechanisms of interaction. All four phenolic substances reduced the level of protein oxidation. Adding 100 μmol/g of RE decreased carbonyl content by 56.16%, enhanced ABTS free radical scavenging rate by 67.34%, and improved digestibility by 33.18%. Noncovalent interactions between polyphenols and MP primarily involved hydrogen bonding and hydrophobic interactions. These interactions preserved the protein's ordered secondary structure, with RE increasing protein solubility by 67.01% under oxidative conditions. These findings suggest that natural polyphenols are effective antioxidants for eel protein, enhancing its functional properties and protecting it against oxidative stress.