The separation of xenon/krypton (Xe/Kr) mixture is of great significance in industry, yet challenging due to their close physical properties. Traditional porous materials typically fail to realize a balance between adsorption capacity and selectivity. Herein, we report a series of water stable fluorinated anion pillared metal-organic frameworks (TIFSIX-Cu-TPA, GeFSIX-Cu-TPA and NbOFFIVE-Cu-TPA) with suitable cages for efficient capture/separation of Xe from Kr. The adsorption capacities of TIFSIX-Cu-TPA, GeFSIX-Cu-TPA and NbOFFIVE-Cu-TPA for Xe at 298 K and 1.0 bar are 64.5, 61.2 and 59.0 STP cm3 g−1, respectively, while those for Kr are only 16.9, 15.8 and 14.9 STP cm3 g−1. Correspondingly, the IAST selectivities for these MOFs are respectively 5.4, 5.3 and 5.1 at 298 K and 1 bar for the Xe/Kr (20/80) mixtures, superior to those of most popular porous materials in the context of Xe/Kr separation. The adsorption heats for Xe are as modest as 22.3, 21.7 and 21.5 kJ/mol for TIFSIX-Cu-TPA, GeFSIX-Cu-TPA and NbOFFIVE-Cu-TPA respectively, indicating the facile conditions for regeneration of the materials. The Xe/Kr binding sites were further studied by Grand Canonical Monte Carlo (GCMC) simulations and density functional theory (DFT) calculations, indicating the preferred binding with Xe over Kr in the large cages decorated with fluorine atoms, corroborating the experimental results. The practical performance of dynamic Xe/Kr separation is further demonstrated by transient breakthrough simulations and experiments.