Effects of silica nanoparticles (SiO2) with different surface properties and their hybrid nanoparticles on the morphology evolution of polyisobutylene (PIB)/polydimethylsiloxane (PDMS) immiscible were are investigated. It shows that the coalescence of dispersed phases can be effectively inhibited by separately adding hydrophilic and hydrophobic nanoparticles. Moreover, adding different ratios of hydrophilic and hydrophobic nanoparticles induces different refinement effects on the droplets of PIB/PDMS 20/80 and 80/20 blends. It is ascribed to the different selective distribution of nanoparticles with different surface properties for PIB/PDMS 20/80 and 80/20 blends. It is suggested that the coalescence of dispersed phases is inhibited by hydrophobic nanoparticles which are dispersed at the interface but located in the matrix phase more effectively than which are dispersed at the interface but located in the dispersed phase.