The 3-isocyanatemethylene-3,5,5-trimethylcyclohexyl isocyanate (IPDI), Polytetrahydrofuran (PTMG2000), Double-tailed hydroxy silicone oil (DSE), 2,2-dihydroxymethyl propionic acid (DMPA) and 1,4-butanediol (BDO) were used as the main raw materials, comb-like organic silicon modified waterborne polyurethane (DSE-WPU) was prepared by prepolymer dispersion method, and then high-strength multifunctional nanocomposite (GO-DSE-WPU) was prepared by adding graphene oxide (GO) slurry, and the relationship between its structure and properties was studied. Mechanical properties analysis showed that the addition of GO and DSE can effectively improve the mechanical properties of GO-DSE-WPU film. Video optical contact Angle analysis shows that, with the increase of GO content, the hydrophobic performance of GO-DSE-WPU film presents a trend of first rising and then declining, and hydrophobicity has improved significantly overall. AFM spectrum analysis explained the reason of the improvement of the hydrophobicity of GO-DSE-WPU from the internal structure. It can be clearly seen from SEM cross-section line sweep energy spectrum that the enrichment rate of silicon on the film-forming surface of GO-DSE-WPU can be increased by 100%. Anti-UV analysis showed that even if a small amount of GO was added, the UV absorption rate of GO-DSE-WPU film was significantly increased and the UV transmittance was significantly reduced. The thermal performance analysis showed that the three thermal degradation temperatures of GO-DSE-WPU were improved compared with that of DSE-WPU, and the thermal performance was improved. Therefore, a multifunctional waterborne polyurethane nanocomposite with high strength can be prepared by this method, which has a wide application prospect in functional coating, surface treatment and film materials.