This study aimed to explore the interaction mechanism between five different polyphenols (caffeic acid (CFA), gallic acid (GA), chlorogenic acid (CHA), resveratrol (RES), and catechin (CAT)) with sea bass myofibrillar protein (MP). The multi-spectroscopy results showed that all five polyphenols could spontaneously form new complexes with MP, with a binding molar ratio of 1:1. The interaction between CFA and MP is predominantly electrostatic, while the interaction between GA and MP is mainly hydrophobic. The rest of polyphenols and MP are mediated by hydrogen bonds and van der Waals forces. And molecular dynamics (MD) simulations indicated that CHA-myosin had the strongest structural stability, while CFA-myosin had the tightest binding. In addition, the amino acid Lys-179 was the key residue for the interaction between five polyphenols and myosin. This study contributes to better understanding the interaction between polyphenols and sea bass MP, which could develop the processing of aquatic food products.