To address the inherent brittleness of conventional transparent conductive oxides, researchers have focused on enhancing their flexibility. This is achieved by incorporating organic films to construct organic-inorganic hybrid layer-by-layer nanostructures, where the interlayer thickness and interface play pivotal roles in determining the properties. These factors are contingent on the type of material, processing conditions, and specific application requirements, making it essential to select the appropriate conditions. In this study, ZnO-zincone nanolaminate thin films were fabricated using atomic layer deposition and molecular layer deposition in various structural configurations. Transmission electron microscopy, X-ray diffraction, and scanning electron microscopy were used to conduct a thorough analysis of the thin-film growth and structural transformations resulting from the deposition conditions. Furthermore, the influence of structural differences at the interfaces on the mechanical properties of the films was investigated by employing both tensile and compression-bending fatigue tests. This comprehensive examination reveals noteworthy variations in the mechanical responses of the films. Thin films characterized by internal porosity and an intermixed amorphous structure demonstrated enhanced compressive toughness, whereas rigid organic layers improved flexibility. These findings offer valuable insights into the development of flexible, transparent multilayer films.