We demonstrate a dialytic strategy for the synthesis of congeneric two-dimensional metal-organic framework (2D MOF) nanosheets with a dialysis membrane using 1,4-benzenedicarboxylic acid (BDC), 1,4-naphthalenedicarboxylic acid (NDC), and 9,10-anthracenedicarboxylic acid (ADC) as organic linkers and copper(II) as a metal precursor, respectively. Polyimide (PI) membranes containing these empty 2D MOF nanosheets exhibit distinct molecular sieve effects. Molecular dynamic simulation results reveal that the structures of MOF-polymer interfaces are designable by modifying the MOF interlayer distance and aperture size, which has significant influences on gas permeability and selectivity. As a result, Cu-NDC/PI with the moderate composite interface structure shows superior performance toward H2/CH4 and CO2/CH4 separations with a selectivity of 199 and 63 over Cu-BDC (121 and 53) and Cu-ADC (135 and 54), respectively.