The morphology change and the corresponding molecular mechanism of polystyrene (PS)/poly(vinyl methyl ether) (PVME) blends induced by hydrophilic or hydrophobic nanoparticles were studied. It was found that there was a threshold of hydrophilic silica loading for the occurrence of network droplet morphological transition in PS/PVME blends. On the contrary, the viscoelastic network could sustain for a much longer time in the blends with higher loading of hydrophobic silica. Rheological measurements suggested that the networking of hydrophilic silica nanoparticles in the PVME-rich phase would significantly reduce the dynamic asymmetry of two phases and make the compositional asymmetry the dominant factor in controlling the morphology development during phase separation. However, adding the hydrophobic silica fillers would result in an increase of dynamic asymmetry and a decrease in compositional asymmetry because of their selective dispersion in the PS-rich phase, both stabilizing the continuous network structure.