Covalent organic frameworks (COFs) are a promising category of porous materials possessing extensive chemical tunability, high porosity, ordered arrangements at a molecular level, and considerable chemical stability. Despite these advantages, the application of COFs as membrane materials for gas separation is limited by their relatively large pore apertures (typically >0.5 nm), which exceed the sieving requirements for most gases whose kinetic diameters are less than 0.4 nm. Herein, we report the fabrication of ultrathin two-dimensional (2D) membranes through layer-by-layer (LbL) assembly of two kinds of ionic covalent organic nanosheets (iCONs) with different pore sizes and opposite charges. Because of the staggered packing of iCONs with strong electrostatic interactions, the resultant membranes exhibit features of reduced aperture size, optimized stacking pattern, and compact dense structure without sacrificing thickness control, which are suitable for molecular sieving gas separation. One of the hybrid membranes, TpEBr@TpPa-SO3Na with a thickness of 41 nm, shows a H2 permeance of 2566 gas permeation units (GPUs) and a H2/CO2 separation factor of 22.6 at 423 K, surpassing the recent Robeson upper bound along with long-term hydrothermal stability. This strategy provides not only a high-performance H2 separation membrane candidate but also an inspiration for pore engineering of COF or 2D porous polymer membranes.