Expanding the utilization of pea protein isolate (PPI)-rutin (Ru) complexes in aerated foods requires a comprehensive understanding of the molecular mechanisms governing their interactions. This study was conducted using multi-spectroscopic techniques, molecular docking, and molecular dynamics simulations and found that the binding mechanism of PPI with Ru involved static quenching. A change in the hydrophobic microenvironment of tryptophan was also confirmed. The primary factors driving the interaction between PPI and Ru were hydrophobic interactions, followed by hydrogen bonding and electrostatic interaction. The most significant contributors to the binding of PPI and Ru were 59ASN, 60LYS, and 63ARG, and their binding promoted the partial unfolding of the secondary structure of PPI. The structural flexibility and surface hydrophobicity of PPI were effectively improved when Ru concentration was 0.1024 mM. The produced foam was characterized by a thicker air/water interfacial film, smaller size, and denser arrangement, resulting in the best foaming properties.