This study demonstrated that a higher efficiency of fumed silica nanoparticles in compatibilizing immiscible polypropylene (PP)/polystyrene (PS) blends can be achieved by replacing a small portion of hydrophobic silica nanoparticles (R974) with hydrophilic ones (A200). Calorimetric and morphological analysis indicated that both hydrophobic and hydrophilic silica nanoparticles possessed good morphological refinement effect on the PP/PS (20/80) blends through different compatibilization mechanisms. The two-step mixing method was more efficient than the one-step mixing method in preparing blends with compatibilized morphology. A higher refinement of the domain size and more profound fractionated crystallization phenomenon in PP/PS blends were observed with simultaneously adding R974 nanosilica and a small amount of A200 nanosilica. This suggested that different compatibilization mechanisms of nanosilica could work synergistically to refine the morphology of polymer blends.