Conventional polymeric membranes face several limitations, such as the trade-off between permeability and selectivity, and physical aging or membrane fouling. In this case, fabrication of composite membranes, usually including mixed matrix membranes (MMMs) or thin film nanocomposite (TFN) membranes by introduction of porous materials as fillers has gained much attention. To achieve excellent membrane performance, it is of great importance to select proper porous materials to avoid agglomeration or precipitation during the composite membrane fabrication processes. Metal-organic cages (MOCs) have been explored as additives for the fabrication of defect-free composite membranes owing to their diversified topologies, well-defined pore structures, nanoscale size, and excellent solubility. This review mainly focuses on the recent advances in applications of MOCs for membrane separation, including synthetic artificial channels, reverse osmosis, nanofiltration, pervaporation and gas separation. Besides, two types of MOCs that have been extensively investigated for composite membrane fabrication are also highlighted. Furthermore, challenges and possible directions are also discussed in details, hoping to provide insightful guidance on the development of more MOC-based membranes with impressive separation performance.