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Metal/covalent-organic framework (MOF/COF) membranes have attracted increasing research interest and have been considered as state-of-the-art platforms applied in various environment- and energy-related separation/transportation processes. To break the trade-off between permeability and selectivity to achieve ultimate separation, recent studies have been oriented towards how to design and exploit ultrathin MOF/COF membranes (i.e. sub-1 μm-thick). Given great advances made in the past five years, it is valuable to timely and systematically summarize the recent development and shed light on the future trend in this multidisciplinary field. In this review, we first present the advanced strategies in fabricating ultrathin defect-free MOF/COF membranes such as in situ growth, contra-diffusion method, layer-by-layer (LBL) assembly, metal-based precursor as the pre-functionalized layer, interface-assisted strategy, and laminated assembly of MOF/COF nanosheets. Then, the recent progress in some emerging applications of ultrathin MOF/COF membranes beyond gas separation is highlighted, including water treatment and seawater desalination, organic solvent nanofiltration, and energy-related separation/transportation (i.e. lithium ion separation and proton conductivity). Finally, some unsolved scientific and technical challenges associated with future perspectives in this field are discussed, inspiring the development of next-generation separation membranes.