Recent study deals with the effect of functionalized Muti-walled carbon nanotube (MWCNT) and other compatibilizers (Closite 6A and Zn++ ion coated nanosilica) on the compatibility and properties of polycarbonate (PC) and Liquid Crystalline Polymer (LCP). The nanocomposites have been melt blended using twin-screw extruder and molded in a compression mold. A remarkable enhancement of thermal, dynamic mechanical properties have been observed with the incorporation of functionalized MWCNT and compatibilizers. Zn++ ion coated nanosilica seems to be more effective as compatibilizer incase of the concerned system. Percent crystallinty associated with the crystallite size have also been increased due to the heterogeneous nucleation of the functionalized MWCNT and compatibilizers. Compatibility between PC and LCP has been studied in terms of particle size determined by Scion Image Analysis in Field Emission Scanning Electron Microscopic (FESEM) study. Dispersion of MWCNT has been exhibited by High Resolution Transmission Electron Microscope (HRTEM).