A series of environmentally friendly and sustainable polyurethanes using epoxy soybean oil as feedstock were synthesized with the introduction of double-decker silsesquioxane. Feature is that through the two-step polymerization, double-decker octaphenylsilsesquioxanetetraol was added to partially replace 1,4-butanediol acting as chain extender, and petroleum-based polyol was effectively replaced for polyurethane synthesis. On top of that, POSS tetraol was prepared and characterized by 1H NMR and MALDI-TOF MS. As for the organic–inorganic hybrid nanocomposites, their structures and properties were investigated by FTIR, DSC, TGA, SEM, tensile test techniques, and static contact angle. DSC analysis showed that covalent incorporation of POSS into the PU network would increase the glass transition temperature (T g) of the systems. TG analysis demonstrated that the hybrid nanocomposites were indeed more oxidative thermal stable, compared to virgin polyurethane especially at high temperature. SEM revealed that both nano- and micro-sized POSS aggregates were shown to be dispersed heterogeneously in the polyurethane matrix, despite the expectation to be dispersed or corporate into molecular chains by chemical bonding between OH and NCO. According to the tensile test results, POSS-containing nanocomposites exhibited an increased modulus with an increasing POSS concentration at low POSS content, and with high loading, these values would decline. The results of the static contact angles revealed that the hydrophobicity of the hybrid material was significantly improved with the inclusion of POSS.