The fine-tuning of the pore structure of metal-organic frameworks (MOFs) is of critical importance to developing energy-efficient processes for the challenging separation of structurally similar molecules. Herein, we demonstrate a strategy to realize a quasi-three-dimensional refinement of the pore structure that utilizes the tunability of ring size and number in polycycloalkane-dicarboxylate ligands. Two hydrolytically stable MOFs with a confined aliphatic pore environment, ZUL-C1 and ZUL-C2, were, for the first time, synthesized and applied in separating low-concentration C2-C3 hydrocarbons from natural gas and ultralow-concentration Xe from used nuclear fuel (UNF) off-gas. Validated by X-ray diffraction and modeling, an expansion of the polycycloalkane moiety enables sub-angstrom contraction in specific directions and forms a pore surface with more alkyl sites, which affords stronger trapping of guest molecules with relatively higher polarizability. The resultant material exhibits record C2H6/CH4 and C3H8/CH4 selectivities coupled with a benchmark low-pressure C2H6 capacity in alkane mixture separation and also a benchmark Xe capacity at extremely diluted feed concentration and record Kr productivity for the Xe/Kr (20:80, v/v) mixture in Xe/Kr separation.