The employment of atomic layer deposition and spin coating techniques for preparing inorganic–organic hybrid multilayer structures of alternating ZnO-CNC layers was explored in this study. Helium ion microscopy and X-ray reflectivity showed the superlattice formation for the nanolaminate structures and atomic force microscopy established the efficient control of the CNCs surface coverage on the Al-doped ΖnO by manipulating the concentration of the spin coating solution. Thickness characterization of the hybrid structures was performed via both ellipsometry and X-ray reflectivity and the thermal conductivity was examined by time domain thermoreflectance technique. It appears that even the incorporation of a limited amount of CNCs between the ZnO laminates strongly suppresses the thermal conductivity. Even small, submonolayer amounts of CNCs worked as a more efficient insulating material than hydroquinone or cellulose nanofibers which have been employed in previous studies.