Isoporous block copolymer membranes are viewed as the next‐generation separation membranes for their unique structures and urgent application in precise separation. However, an obvious weakness for such membranes is their poor solvent‐resistance which limits their applications to aqueous solution, and isoporous membranes with superior solvent‐resistance and tunable pore size have been rarely prepared before. Herein, self‐supporting isoporous membranes with excellent solvent resistance are prepared by the facile yet robust hyper‐crosslinking approach which is able to create a rigid network in whole membranes. The hyper‐crosslinking is found to be a novel and non‐destructive approach that does not change pore size and isoporous structure during the reaction, and the resulting hyper‐crosslinked isoporous membranes display superior structural and separation stability to a broad range of solvents with varied polarities for months to years. More importantly, hyper‐crosslinking has proved to be a universal strategy that is applicable to isoporous membranes with varied pore size and pore chemistry, offering an important opportunity to prepare solvent‐resistant isoporous membranes with customizable pore size and pore functionality that are important to realize their accurate separations in organic solvents. This concept is demonstrated finally by precise and on‐demand separation of nanoparticles with the prepared membranes.