The reduced antioxidant capacity of trans-resveratrol (Res) than the second generation of Res, namely pterostilbene (Pte), severely prohibits its in-depth intriguing radical-scavenging applications in food formulations. Herein, a unique chemical structure-dependent strategy was proposed to specifically enhance the radical scavenging activity of Res over Pte, relying on the two more hydroxyl groups on the A-benzene ring of Res, thus facilitating its binding with lactoferrin (LF) to form stable complexes through more hydrogen bonds. We prepared LF-Res and LF-Pte complexes, revealed their binding mechanisms by multispectral analysis and molecular docking/dynamics simulations, further evaluated their antioxidant properties via ABTS and DPPH assays and a model of inhibiting apple browning, eventually elucidated their structure-binding-property relationships. This contribution offers a new approach to restore the antioxidant capability of Res, also paves the way to precisely regulate the fascinating bioactivities of hydrophobic compounds by protein-binding in a chemical structure-, especially hydroxyl group-dependent manner.