A series of waterborne polyurethane-silica (WPUS) crosslinked hybrid dispersions were prepared based on polyoxytetramethylene glycol (PTMG) and isophorone diisocyanate (IPDI) as the raw materials, with 2-hydroxyethyl methacrylate (HEMA) and pentaerythritol triacrylate (PETA) as grafting reagents and (3-mercaptopropyl)triethoxysilane (MPTES) as the coupling agent. SiO2 nanoparticles that functioned as a nanofiller were introduced by a novel click chemistry method. Crosslinked networks were constructed in the WPUS, with SiO2 acting as the crosslinks. The effects of the amount of SiO2 on the properties of the WPUS nanocomposites were investigated. It was found that WPUS films exhibited admirable thermal properties due to their crosslinked structure. Contact angle tests and water absorption rate measurement results demonstrated the hydrophobicity of WPUS films are obviously enhanced, because of the migration and crosslinked of highly hydrophobic silicon which has lower surface energy during the film formation. Meanwhile, SiO2 as a crosslinker and reinforcing filler, which affects the mechanical tensile in this system, the tensile strength of the WPUS increased from 10.45 MPa to 24.10 MPa with increased amounts of SiO2. The performances of the WPUS composite material top the most, when the amount of SiO2 is 2.5 wt%.