A flexible hard coating material displaying extreme scratch resistance and foldable flexibility was developed via the design of an organic-inorganic hybrid coating material employing an alkoxysilyl-functionalized polyrotaxane cross-linker (PRX_Si1). PRX_Si1 has a molecular necklace-like structure that can form organic-inorganic cross-linking points and provide large molecular movements. It was postulated that the scratch resistance and flexibility could be simultaneously increased because of the hybrid cross-linking points and dynamic molecular movements. To confirm this hypothesis, the crystalline structure and mechanical properties of the PRX_Si1-based hard coating material were analyzed via transmission electron microscopy, small-angle X-ray diffraction, tensile, pencil hardness, and scratch tests. Finally, the PRX_Si1-based hard coating material could form homogeneously dispersed nanoscale siloxane crystalline domains, and the strain at the break point was 3 times higher than that of a commercial hard coating material, resulting in no defect formation even after 5000 folding test runs. Moreover, the material displayed extremely high pencil hardness (9H) and scratch resistance.