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A three-dimensional copper metal-organic framework with the rare chabazite (CHA) topology namely FJI-Y11 has been constructed with flexibly carboxylic ligand 5,5'-[(1,4-phenylenebis(methylene))bis(oxy)]diisophthalic acid (H4L).FJI-Y11 exhibits high water stability with the pH range from 2 to 12 at temperature as high as 373 K.Importantly,FJI-Y11 also shows high efficiency of hydrogen isotope separation using dynamic column breakthrough experiments under atmospheric pressure at 77 K.Attributed to its excellent structural stability,FJI-Y11 possesses good regenerated performance and maintains high separation efficiency after three cycles of breakthrough experiments.