High performance carbon nanotube (CNT) nanopaper (NP) reinforced polyurethane (PU) nanocomposite coating with high potential for aerospace and automotive applications was successfully fabricated and evaluated in this work. Different PU formulations were used to fabricate nanocomposites to study the effect of hard segment content on resin infiltration and nanocomposite mechanical properties. The process window of PU infiltration into the CNT NP was established by rheology measurements and thermal gravimetric analysis (TGA). The micro-structure morphology of the nanocomposite was characterized by scanning electron microscope (SEM). Uniform CNT distribution in PU matrix was observed in the high-resolution SEM images, which indicated good resin impregnation quality. Based on mechanical properties and process window, a PU formulation was selected as matrix to fabricate NP/PU nanocomposite coating for carbon fiber/epoxy composites (CFPC) substrate. The flexural strength and impact resistance of the CFPC were significantly improved by 9% and 14.7% after applying the NP/PU nanocomposite coating. Aimed at industrial applications, a continuous nanopaper fabrication process was successfully demonstrated in this work. Through the process window study, a continuous process to fabricate nanocomposite is proposed for future scale-up.