The influence of shear flow on the nanomechanical properties of cellulose nanocrystal (CNC)/polyethylene glycol (PEG) composite films and the distribution of anisotropic phases are investigated at various CNC/PEG ratios. Here, the drying process of CNC/PEG mixed suspensions is systematically traced by rheology, followed by the spatial mapping of local mechanical properties of CNC/PEG films by nanoindentation. The detailed study of the morphology of CNC/PEG films by polarized optical microscopy (POM) and image analysis revealed the link between the mechanical properties and the influence of shear flow. A comparison of the data obtained for shear-dried films with nonsheared films showed the improved reduced Young's modulus (Er) and hardness (H), and suppression of microphase separation in the shear-dried films. Based on this experimental evidence, a mechanism is proposed to explain the microstructural transition during the shear-drying process leading to the generation of the anisotropic domains containing the shear-induced assembled structure of CNC particles coexisting with the elongated PEG microphases.