Shifting from petroleum-based feedstocks to renewable biomass for high-performance waterborne polyurethane (WPU) coatings is critical for promoting sustainability within the coatings industry. In this work, castor oil (CO) was chemically modified with cinnamic acid (CA) to produce a customized polyol featuring precisely three hydroxyl groups, three benzene rings, and three carboxyl groups per molecule. This functionalized-CO was employed as the soft segment and was combined with L-lysine diisocyanate as the hard segment, protocatechuic acid (PA) as the chain extender, and gallic acid (GA) as an intramolecular cross-linker to synthesize a series of bio-based WPU coatings intended for application on oak wood (Xylosma congesta). The benzene ring of GA functions as a 3D cross-linking node, transforming the quasi-one-dimensional π–π stacking interactions between the CA and PA benzene rings along the polymer backbone into an interconnected 3D aromatic conjugated network. This synergistic interaction between covalent cross-linking and physical π–π stacking enhances multiple material properties simultaneously, including tensile strength (30.9 MPa), thermal stability (T5% = 289.4 °C), storage modulus (3815.6 MPa), toughness (87.9 MJ·m⁻3), solvent resistance, and microphase separation, while maintaining significant biodegradability under both soil burial and enzymatic degradation conditions. When applied to oak wood substrates, the coatings reduced abrasion-induced mass loss from 117 mg to 13 mg and lowered the water vapor transmission rate to 35.2 g·m⁻2·24h⁻1, outperforming two commercial WPU products used as benchmarks across evaluated parameters. This research establishes a comprehensive structure–property framework based on the interplay between covalent cross-linking and supramolecular π–π stacking, providing molecular-level design guidelines for the development of fully bio-based, high-performance wood coatings.