Recycling water-soluble ionic liquids (ILs) from dilute aqueous solutions using nanofiltration membranes has garnered substantial attention due to the potential environmental impact and relatively high cost associated with ILs, which limit sustainable development. However, conventional polyamide nanofiltration membranes exhibit less attractive separation performance, limiting their widespread adoption. In this study, we present, for the first time, a series of covalent organic framework (COF) membranes designed with angstrom-level pore size discrimination and highly tunable charge distribution on the membrane surface for the nanofiltration of water-soluble IL at a concentration of 0.05 mol L −1 . These COF membranes demonstrate exceptional IL rejection rates (>90%) and outstanding cycling stability by combining precisely controlled pore size and a negatively charged membrane surface. Mechanistic studies reveal that angstromlevel pore size discrimination enhances the molecular sieve process, and the tunable surface charge distribution enhances electrostatic repulsion. Furthermore, the remarkable nanomechanical properties of the COF membranes ensure their durability. This work underscores the feasibility of engineering the pore size and charge properties of COF membranes at the molecular level to achieve high-performance IL nanofiltration.