Two-dimensional covalent organic frameworks (2D COFs) are considered as potential candidates for gas separation membranes, benefiting from permanent porosity, light-weight skeletons, excellent stability and facilely-tailored functionalities. However, their pore sizes are generally larger than the kinetic diameters of common gas molecules. One great challenge is the fabrication of single-phase COF membranes to realize precise gas separations. Herein, three kinds of high-quality β-ketoenamine-type COF nanosheets with different pore sizes were developed and aggregated to ultrathin nanosheet membranes with distinctive staggered stacking patterns. The narrowed pore sizes derived from the micro-structures and selective adsorption capacities synergistically endowed the COF membranes with intriguing CO2 -philic separation performances, among which TpPa-2 with medium pore size exhibited an optimal CO2 /H2 separation factor of 22 and a CO2 permeance of 328 gas permeation units at 298 K. This membrane performance reached the target with commercial feasibility for syngas separations.