Although the morphological refinement and mechanical enhancement effect of hydrophobic nanoparticles on immiscible polymer blends been frequently reported, the hydrophobicity of nanoparticles on the morphological evolution of these complex systems under flows is still unrevealed. Firstly, the morphological stability of polypropylene/polystyrene (PP/PS) blends filled with nanoparticles with different hydrophobicity under simple shear flow via online optical-shear technique. At high shear rates, the coalescence dynamics of droplets was suppressed in the presence of nanosilica with different hydrophobicity. When imposing a slow shear flow, the stability of the refined morphology for nanosilica-filled blends was changed with the nanosilica hydrophobicity due to its selective distribution. Then, the influence of nanosilica with different hydrophobicity on the morphology-rheology correlation of PP/PS blends was studied in simple elongational flow. In elongation, the morphology was deformed or stable, depending on the hydrophobicity of nanosilica. The discrepancies in the morphology deformation were ascribed to the difference in the selective distributions of nanosilica with different hydrophobicity. Some novel phenomena were found in elongational rheology of these nanosilica-filled blends and interpreted in terms of the interfacially confined distribution of nanosilica. This work was supported by the National Natural Science Foundation of China (51503133, 51373109, 51721091). Keywords: blends; nanoparticles; morphology; shear; elongation