Comprehensive comprehension of the interaction between proteins and polyphenols is crucial for advancing their utilization in food processing. This study investigated no-covalent interaction between pea protein isolate (PPI) and quercetin (Que) through spectroscopic analysis and molecular simulation. Fourier transform infrared spectroscopy and circular dichroism spectrum showed that the interaction between PPI and Que changed the secondary structure of the protein due to a decrease in α-helix content and an increase in the random coil. Thermodynamic parameters indicated that the Quebound PPI via hydrogen bonds and hydrophobic interactions (ΔH>0, ΔS>0, and ΔG<0), which was also confirmed by molecular docking. Particle size and ζ-potential showed that PPI and Que demonstrated effective interaction and binding capabilities, enhancing the stability. In addition, the antioxidant and bioaccessibility of complexes have also been enhanced. This study shed a light on the application of protein-polyphenol complexes for developing functional foods. PRACTICAL APPLICATION: Interaction between pea protein isolate and quercetin can change the protein conformation to maintain the stability of quercetin and is helpful to expand the market value and application value of plant protein. The research has important implications for using leguminous protein as embedded support to improve the stability of polyphenols compounds.