Multiple space from the interior of metal-organic polyhedra (MOPs), the exterior among MOPs, and the inherent nature of big organic molecules makes MOPs as promising platform with hierarchical porous structures, especially when well-elucidated reticular chemistry principles were used. Herein we describe the preparation of a series of isoreticular octahedral MOPs featuring Zn₄-p-tert-butylsulfonylcalix[4]arene clusters by the metal-directed assembly of three rigid organic ligands with different lengths. Intercage hydrogen-bonds and hydrophobic interactions between sulfonylcalix[4]arene groups direct the stacking of discrete MOPs into a novel permanent hierarchical porous material. More importantly, the optimal MOP 1-Zn exhibits high adsorption capacity of Xe and excellent Xe/Kr (20/80, v/v) separation performance, as demonstrated by adsorption isotherms, breakthrough experiments, and density functional theory calculations. Additionally, grand canonical Monte Carlo (GCMC) and dispersion-corrected density functional theory (DFT-D) theoretical calculations provide molecular-level insight over the adsorption/separation mechanism.