Membrane‐based gas separations are energy efficient processes; however, major challenges remain to develop high‐performance membranes enabling the replacement of conventional separation processes. Herein, a new fluorinated MOF‐based mixed‐matrix membrane is reported, which is formed by incorporating the MOF crystals into selected polymers via a facile mixed‐matrix approach. By finely controlling the molecular transport in the channels through the MOF apertures tuned by metal pillars and at the MOF‐polymer interfaces, the resulting fluorinated MOF‐based membranes exhibit excellent molecular sieving properties. These materials significantly outperform state‐of‐the‐art membranes for simultaneous removal of H2S and CO2 from natural gas—a challenging and economically important application. The robust fluorinated MOFs (NbOFFIVE‐1‐Ni, AlFFIVE‐1‐Ni), pave a way to efficient membrane separation processes that require precise discrimination of closely sized molecules.​