Flow-induced alignment of shape-anisotropic colloidal particles is of great importance in fundamental research and in the fabrication of structurally anisotropic materials; however, rheo-optical studies of shear-induced particle orientation are time- and labor-intensive and require complicated experimental setups. We report a single-droplet oscillatory microfluidic strategy integrated with in-line polarized light imaging as a strategy for studies of shear-induced alignment of rod-shape nanoparticles. Using an oscillating droplet of an aqueous isotropic suspension of cellulose nanocrystals (CNCs), we explore the effect of the shear rate and suspension viscosity on the flow-induced CNC alignment and subsequent relaxation to the isotropic state. The proposed microfluidic strategy enables high-throughput studies of shear-induced orientations in structured liquid under precisely controlled experimental conditions. The results of such studies can be used in the development of structure-anisotropic materials.