With the implementation of the “plastic restriction order” and the demand for sustainable society development, biodegradable coatings derived from biomass materials have garnered significant interest. This study presents the synthesis of a double‐salt bio‐based waterborne polyurethane (PLA‐WPU) by utilizing poly(lactic acid) polyol (PLA) and isophorone diisocyanate (IPDI) as the main raw materials, along with 2,2‐dihydroxymethylpropionic acid (DMPA) and sodium ethylenediamine ethanesulfonate (A‐95) as a hydrophilic chain extender. Synergistic reinforcement of PLA‐WPU using hydrophobically modified cellulose nanocrystals (M‐CNC) and polycarbonate diimide (PDCDA). At an M‐CNC content of 3% relative to the effective mass of PLA‐WPU, the tensile strength reached 36.12 MPa. After 8 days a lipase PBS solution, the degradation rate reached 54%. Excellent waterproof performance was observed, exhibiting a contact angle of 143.5°. When applied as a surface coating on kraft paper, the Cobb 60 value decreased from 74.0 to 28.6 g/m2, while increasing the tensile strength by 451.3%. Importantly, the kraft paper maintained excellent waterproofing, mechanical strength, and high barrier properties even after repeated folding, high and low‐temperature conditions, and exposure to varying pH solutions. It proved to be both degradable and recyclable, making it a promising alternative to liner paper or plastic membrane, especially in food packaging.