The need of isotopic compounds has been rising in recent years for both medical applications and scientific research. Existing technologies (e.g., cryogenic distillation, Girdler sulfide process, and supersonic beam diffraction) have difficulties to meet the growing global demand for enriching pure isotopic compounds because of low separation capacity, poor selectivity, and large energy consumptions. Metal−organic frameworks (MOFs) have been demonstrated promising for separation of isotopic compounds because of their tunable pore sizes and chemical affinities. In this work, we theoretically investigate 4764 experimentally synthesized MOFs for their potential applications in the separation of three representative isotopic methane pairs selected on the basis of their differences in molecular size, interaction energy, and a combination of both size and energy characteristics. Top MOF candidates have been identified with highest adsorption performance scores, highest adsorption selectivity, and highest membrane selectivity. The theoretical results suggest that MOF adsorption provides the selectivity of isotopic methanes, which is significantly larger than conventional separation methods. While isotopic separation by adsorption alone is compromised by a small working capacity, utilization of MOFs as a porous membrane facilitates efficient separation of isotopic methanes with both high working capacity (permeability) and large selectivity.