Hydrophilic silica nanoparticles were introduced into the epoxy/polyetherimide (epoxy/PEI) binary system to study their effect on the reaction induced phase separation (RIPS) by differential scanning calorimetry (DSC), optical microscopy (OM), and time-resolved light scattering (TRLS). Depending on the specific interaction between the silica surface and the epoxy, the silica nanoparticles selectively distribute in the epoxy-rich domain, leading to a slow down of the diffusion of the epoxy molecules. And the coarsening mechanism was forced towards the diffusion-controlled regime, which enhanced the viscoelastic effect and produced a more dynamic asymmetric epoxy/PEI system. Based on this, the final morphology was stopped at an earlier stage of an inverted phase structure (isolated epoxy-rich droplet and PEI-rich matrix). The silica nanoparticles showed a critical impact on the balance of the diffusion and geometrical growth of epoxy molecules. Further, the activity energy of the curing reaction and the phase separation temperatures were decreased by existence of the silica nanoparticles.