The presence of various trace water-soluble organic pollutants, such as dyes, poses significant potential risks to human health and ecosystems. Membrane technology presents a promising and sustainable approach for their removal from aqueous environments. However, the amorphous structure of most commercial membranes makes it challenging to achieve effective separation with high water flux. Here, we present a novel series of hydrophilic COF membranes with different alkoxy sidechain lengths for the first time. These alkoxy sidechain functional COF membranes exhibit efficient rejection of water-soluble organic dyes, including rose bengal (> 50 %), congo red (> 98 %), brilliant blue R250 (> 99 %), and alcian blue (> 99 %). Moreover, these membranes demonstrate a high water flux exceeding 291.8 L m-2h−1 bar−1 and exceptional long-term operational stability lasting at least 2880 min. The superior performance of COF membranes is attributed to their optimal pore size, excellent hydrophilicity, and high crystallinity. This finding offers a promising approach for effectively eliminating water-soluble organic pollutants, thereby ensuring the safety and sustainability of the water supply.