Two-dimensional covalent organic frameworks (COFs) with uniform pores and large surface areas are ideal candidates for constructing advanced molecular sieving membranes. However, a fabrication strategy to synthesize a free-standing COF membrane with a high permselectivity has not been fully explored yet. Herein, we prepared a free-standing TpPa-SO3H COF membrane with vertically aligned one-dimensional nanochannels. The introduction of the sulfonic acid groups on the COF membrane provides abundant negative charge sites in its pore wall, which achieve a high water flux and an excellent sieving performance toward water-soluble drugs and dyes with different charges and sizes. Furthermore, the COF membrane exhibited long-term stability, fouling resistance, and recyclability in rejection performance. We envisage that this work provides new insights into the effect of ionic ligands on the design of a broad range of COF membranes for advanced separation applications.