Waterborne polyurethane (WPU) coatings with antibacterial properties have attracted extensive attention. Herein, we proposed a molecular design strategy was used to establish a series of castor oil/tung oil based WPU antibacterial coatings. By introducing conjugated double bonds of tung oil into WPU skeleton, electrostatic interaction by zwitterion and bacterial division inhibition by conjugated double bonds achieved the synergistic antibacterial effects. To our delight, inspired by lotus leaves, the scanning electron microscope test revealed the bionic micro-nano embedded structure was constructed on the surface of WPU using siloxane-modified nanocellulose (CNC@MTES). The destruction of the phosphorus layers and superhydrophobicity grant the material to have quadruple synergistic antibacterial effects. The antibacterial rates of WPU coatings on E. coli and S. aureus were more than 99.6% and played the mildew protection effect. What's more, peroxy bond formed by unique oxidative cross-linking induced self-reinforcing to enhanced the mechanical properties (the stress and Young's modulus of coating enhanced by 122.06% and 2368% respectively). Strong bonding between CNC@MTES and WPU ensured the durability of the coating, which was still effectively antibacterial and hydrophobic after 400 friction cycles. This research offered an innovative and effective method for coating to be widely used in product packaging, medical devices, smart glass and other fields.