Thin-film composite nanofiltration (TFC NF) membranes can separate neutral/charged solutes and play an essential role in water purification. However, the permeability of traditional NF membranes is severely limited by excessive mass transfer resistance due to the thick polyamide (PA) layer. Introducing porous nanomaterials as an interlayer into PA NF membranes has been recognized as an effective approach to improve permeability. Herein, a novel composite interlayer consisting of anionic covalent organic frameworks with abundant sulfonic acid groups (COF-SO3H) and polydopamine was designed to regulate interfacial polymerization to construct the highly permeable TFC NF membranes. The surface negative charge and hydrophilicity of the TFC NF membranes can be controlled by the abundant polar groups in the composite interlayer. Moreover, mass transfer resistance can be reduced by introducing COF-SO3H to create additional water transport channels. The results showed that the optimal membrane manifested attractive permeability (44.2 L⋅m−2⋅h−1⋅bar−1) and a high Na2SO4 rejection (98.7 %), almost 3-fold higher than that of the original TFC membrane. Furthermore, the optimal membrane exhibited favorable anti-fouling performance and stability. This work provides insight into strategies for fabricating highly permeable TFC NF membranes through the introduction of an interlayer.