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Nanoporous materials exhibit remarkable mechanical properties, which are influenced by their surface effects and microstructures. Here, we theoretically analyze Young’s modulus of various regular polygonal prism structures, which represent the first-level (conventional) nanoporous material and higher-level hierarchical nanoporous material. The effects of surface elastic modulus, porosity, residual surface stress, and side number on Young’s modulus of a regular polygonal prism unit cell are investigated in detail. The results reveal that Young’s modulus is controlled by the surface elastic modulus, but it is not sensitive to the residual surface stress. This trend is in good consistency with the existing work. Moreover, the effective modulus strongly depends upon the surface elastic modulus. Under the certain range of high porosity, maximum Young’s modulus always relies on a critical side number of 6, regardless of the surface effect and hierarchical structure. Interestingly, for different regular polygonal prism structures, the difference in effective modulus tends to decrease with the increasing porosity. The current findings provide insights to improve the mechanical properties of nanoporous materials via tuning microstructure, porosity, and surface elastic modulus.