Many membranes with various pore structures have been studied for size-based selective filtration and separation. However, one exhibiting reverse size selectivity has rarely been reported. Here, we present a facile synthesis of a hierarchically nanoporous covalent framework (NCF) membranes using concurrent phase separation and gelation of the mixtures of a urea-linked network (UN) sol, poly (ethylene glycol) (PEG), and ionic liquid (IL). Subsequent solvent extraction of the dual porogens, i.e., PEG and IL, from the ternary blend gave a hierarchically nanoporous structure consisting of a continuous macropore running across a continuous mesoporous framework. The structure formation was accounted for by the primary separation of the IL-rich phase, followed by the secondary separation of the PEG domain from the continuous UN skeleton. The porosity and pore distribution of the membrane was varied by adjusting the composition of the PEG/IL/UN mixture. The hierarchical nanoporosity provided a reverse size selectivity for the ultrafiltration of proteins and polymers, promising potential applications in membrane-based protein purification or chromatography.