To combat global warming, as an energy-saving technology, membrane separation can be applied to capture CO2 from flue gas. Metal–organic frameworks (MOFs) with characteristics like high porosity have great potential as membrane materials for gas mixture separation. In this work, through a combination of grand canonical Monte Carlo and molecular dynamics simulations, the permeability of three gases (CO2, N2, and O2) was calculated and estimated in 6013 computation–ready experimental MOF membranes (CoRE–MOFMs). Then, the relationship between structural descriptors and permeance performance, and the importance of available permeance area to permeance performance of gas molecules with smaller kinetic diameters were found by univariate analysis. Furthermore, comparing the prediction accuracy of seven classification machine learning algorithms, XGBoost was selected to analyze the order of importance of six structural descriptors to permeance performance, through which the conclusion of the univariate analysis was demonstrated one more time. Finally, seven promising CoRE-MOFMs were selected, and their structural characteristics were analyzed. This work provides explicit directions and powerful guidelines to experimenters to accelerate the research on membrane separation for the purification of flue gas.