In the present study, compatibilization of immiscible blends of polymers was investigated based on the Pickering emulsion concept with various mixing procedures. Silica nanoparticles were incorporated into poly (1,4-cyclohexanedimethylene isosorbide terephthalate) (PEICT)/isotactic polypropylene (iPP) blends. Localization of nanoparticles was effectively modified by varying mixing procedures. Relocation of hydrophilic silica occurred in a secondary mixing procedure with the PEICT, which has relatively high affinity when primarily mixed withiPP. The final location of the silica nanoparticles was confirmed by SEM images. SEM and an optical microscope were used to follow morphological change. By simply changing the mixing procedure, the hydrophilic silica nanoparticles were able to perform the role of a morphology modifier successfully without modifying the surface characteristics. The mechanical properties and crystallization behavior were also compared depending on the surface characteristics of the silica nanoparticles and their final localization.