Covalent organic frameworks (COFs) featuring uniform topological structure and devisable functionality have emerged as promising membrane materials. The design and precise manipulation of COF membranes with advanced spatial structure to achieve efficient liquid molecular separations are of great necessity. Herein, zwitterionic COF membranes have been in-situ fabricated on porous polymeric substrates using an interfacial polymerization modification strategy. The continuous defect-free COF membranes with two-dimensional in-plane dominant growth can be achieved by optimizing the fabrication parameters including reaction time, monomer concentration, and catalyst concentration. Subsequent zwitterionic modification thereon not only favors the formation of hydrophilic surface but also improves the sieving capability by sheltering effect. Attributed to the synergistic contribution, the optimized zwitterionic COF membrane possesses a superior separation factor of 2839 with the water content in the permeate up to 99.7 wt%, while maintaining a comparable permeation flux of 3309 g m−2 h−1 during the ethanol dehydration process, outperforming most of other representative membranes. Furthermore, the excellent durability of the zwitterionic COF membrane in the ethanol dehydration process and its efficient separation performance towards other alcohol dehydration systems demonstrate its potential practical applications. The easy scalability of the fabrication and regulation method offers crucial guidance for the engineering of advanced COF membranes in efficient liquid molecular separations.