The isocyanate-functionalized silica nanoparticles were chemically incorporated into the polyurethane (PU) during the synthesis of flexible PU foam from polypropylene glycol and toluene diisocyanate following the one-shot method with water as the blowing agent. Chemical incorporations of silica nanoparticles augmented hardness, initial modulus, and strength for tensile and compression loading. As results, shape fixity, shape recovery, and strain energy storage significantly increased with reduced hysteresis loss. It was found that the chemically incorporated silica particles effectively reinforce the PUs with improved dispersion and act as multifunctional cross-links, elastic energy storage, and relaxation retarder, which are beyond the conventional reinforcing filler. The maximum increases of dynamic properties and shape memory performances with 2% silica are an indication that the chemical incorporation is also limited by particle aggregations, though it appears at higher content than the simple blend.