Application of shear stress has been shown to unidirectionally orient the microstructures of block copolymers and polymer blends. In the present work, we study the phase separation of a novel nanoparticle (NP)-polymer blend thin film system under shear using a soft-shear dynamic zone annealing (DZA-SS) method. The nanoparticles are densely grafted with polymer chains of chemically dissimilar composition from the matrix polymer, which induces phase separation upon thermal annealing into concentrated nanoparticle domains. We systematically examine the influence of DZA-SS translation speed and thus the effective shear rate on nanoparticle domain elongation and compare this with the counterpart binary polymer blend behavior. Unidirectionally aligned nanoparticle string-domains are fabricated in the presence of soft-shear in confined thin film geometry. We expect this DZA-SS method to be applicable to various NP-polymer blends towards unidirectionally aligned nanoparticle structures, which are important to functional nanoparticle structure fabrication.