Robust mechanical property is fundamentally significant for applications of nano‐materials, such as micro‐fluidic, sensor, superhydrophobic/ icephobic, and crush‐resistant functions. However, the nano‐materials used in the applications are always easily ruined due to the poor adhesion and weak mechanical properties. To enhance the nano‐materials’ duration in hash environment, a strategy of robust nano‐topography protection is studied in this paper. In our experiment, a series of multi‐level sub‐mm topography with nano‐materials are fabricated by integrating the methods of soft lithography, and crystal growth. The mechanical properties of nano‐materials are quantitatively studied, and the nano‐material can be protected by the designed flexible multi‐level topography, which significantly decreases the strain and stress of the nano‐structure. To investigate the mechanism of this performance, a series of simulations are performed, and a mechanical model is established to explain this phenomenon. This work uncovers the multi‐level principles for nano‐materials protection and gives a guideline to design the nano‐materials’ surfaces.