Covalent organic frameworks (COFs) are emergent ideal membrane materials, owing to their pre-designable and well-defined pore structures. However, COFs typically exist as solid powder and are hard to dissolve in most solvent, which renders COFs poor processability in membrane formation. In this study, TpPa-SO3H/PAN COF membranes (COFMs) were prepared via counter diffusion method, which is modulated by the pre-assembled two-dimensional (2D) crystalline TpPa-SO3H nanosheets as seeding layer. The TpPa-SO3H seeding layer regulated the diffusion-reaction behavior of monomers and induced the confined growth of TpPa-SO3H COFs, which is favorable for eliminating the intergranular defects inside the TpPa-SO3H/PAN COFMs. The thickness of TpPa-SO3H seeding layer can be controlled by the amount of TpPa-SO3H nanosheets. The charge of the channel wall inside the membrane can fortify the electrostatic repulsion mechanism and facilitate efficient desalination. Under the optimal conditions, the Na2SO4 rejection rate of TpPa-SO3H/PAN COFMs can reach 97.4%. Unlike conventional polyamide membranes whose desalination performance usually decreases with the increase of salt concentration, the TpPa-SO3H/PAN COFMs preserved superior desalination performance toward high salt concentration up to 10,000 ppm.