A series of cottonseed oil based waterborne polyurethane–silica (CSOWPU–Si) hybrid materials were prepared via the chemically interaction between NCO groups of polyurethane prepolymer and the surface of 3-aminopropyl trimethoxysilane (APTMS). The biobased triglyceride oils were first epoxidized cottonseed oil followed by oxirane ring-opened with varying polyhydroxy (OH) fatty acid numbers. The attached modified APTMS thus performed the dual roles not only chain extender filler but including reinforcing agent in the resulting hybrid coatings. Fourier transform infrared spectra expose the crosslinking interaction between polyurethane and the appearance of silica nanoparticles in the polymer matrix. The 29Si solid-state NMR spectra sign the formation and the behavior of siloxane linkage in the CSOWPU–Si nanocomposites films. Dynamic mechanical analysis (DMA) studies show that the appearance of silica nanoparticles provides rigidity to CSOWPU–Si film, thereby enhancing the storage modulus. The effect of crosslinking density and thermophysical and mechanical properties of the polyurethane and the resulting hybrid materials films was evaluated by the differential scanning calorimetry (DSC), thermal gravimetric analysis (TGA), and measurement of the mechanical properties. This work renders a new effective and promising route of utilizing biorenewable for the development of CSOWPU–Si hybrid materials with high performance coating applications.