Antimicrobial peptide Pup2, due to high cost, shows restricted application value in food preservative, which may be improved by interacting with EGCG, characterized by good functional properties. This study aims to characterize a novel antimicrobial peptide-phenolic complex with activity against Staphylococcus aureus and investigate their interaction mechanism. Pup2 and Epigallocatechin-3-gallate (EGCG) exhibited synergistic effects, resulting in a 4-fold and 8-fold decrease in the minimum inhibitory concentration, respectively. Furthermore, the Pup2/EGCG showed a synergistic damaging effect on the bacterial cell wall and membranes. Multi-spectroscopic analyses, which included UV, fluorescence, FTIR, and Raman spectroscopy, showed that Pup2 and EGCG were non-covalently bound through hydrophobic interactions predominantly and assisted by hydrogen bonding. These interactions led to changes in the amino acid microenvironment of Pup2 and alterations in its secondary structure, with the α-helix content increasing from 3% to 26%. DSC similarly confirmed the occurrence of interactions and increased peptide stability. Additionally, molecular simulations further demonstrated hydrophobic interaction and hydrogen bonding were the main binding forces between Pup2 and EGCG, resulting in the formation of a stable complex. This study helps to elucidate the interaction mechanism between antimicrobial peptide Pup2 and EGCG at the molecular level, while highlights the potential application of this complex as a more economical and effective natural antimicrobial preservative.