Covalent organic frameworks (COFs) membranes have exhibited great applications in wastewater treatment due to their highly ordered porous architecture. Currently, numerous studies have focused on the hexagonal-structured COFs synthesized with linear C2 and C3 precursor. However, the C2 monomer is limited-variety and high-cost. Herein, a novel clover-like structure COFs membrane is successfully fabricated for the first time. Meta-position monomer m-phenylenediamine (MPD) and 1,3,5-triformylbenzene (TFB) are used to synthesize the clover-like COFs membrane by interfacial polymerization (IP) method on the nylon substrate directly. The optimized MPD-TFB/Nylon membrane shows excellent water permeance of 94.4 L m−2 h−1 bar−1, which is higher than hexagonal-structured COFs membrane, in Congo red (CR) and NaCl mixed solution The rejections are 98.6% for CR and 2.9% for NaCl. This work opens a novel route for designing the COFs membrane with clover-like channels, manifesting the usage of linear C2 monomers is unnecessary. Besides, it has been found that the unique clover-like structure can improve the water molecular transport path under the same dye molecules deposition situation compared with hexagonal structure COFs membrane.