We demonstrated a novel nanoparticle (NP) self-assembly method in a liquid crystal (LC) medium by exploiting two physical phenomena: (i) surface affinity contrast of isotropic pockets in nematic phase for ITO and self-assembled monolayer (SAM), and (ii) NP solubility contrast in isotropic and nematic phase. In the former phenomenon, the higher molecular roughness of ITO surface than SAM surface induced the higher surface affinity of isotropic pockets on the ITO surface. Hence, the isotropic pockets were anchored on the ITO islands of the patterned ITO substrate, while the nematic medium remained on the other area in which SAM was created. In the latter phenomenon, the uni-directional alignment in the bulk LC of nematic phase was mismatched with the one on the NP interface while the isotropic phase did not show any mismatch between the LC alignment in bulk and at the NP interface. The alignment mismatch in nematic phase resulted in the poorer NP solubility than it in isotropic phase. Hence, this large NP solubility contrast in two phases resulted in the NPs were confined to the isotropic pockets and dragged by the phase-boundary. By combining the two phenomena, we successfully fabricated the self-assembled NP cluster array on the ITO islands of the patterned ITO substrate. Since no electric or magnetic field is used in this method, it is applicable to a wide variety of NPs including ferroelectric, ferromagnetic etc. This method can potentially be utilized for fabrication of photonic crystals.