This study synthesizes sulfonated covalent organic framework nanosheets (S-CONs) and incorporates them into a polyamide (PA) layer via interfacial polymerization to create thin-film nanocomposite (TFN) nanofiltration (NF) membranes. The S-CONs enhance membrane hydrophilicity, reduce PA layer thickness, and increase surface electronegativity, leading to improved pure water permeance (8.84 L·m⁻²·h⁻¹·bar⁻¹, 1.75 times higher than the TFC membrane) and Na₂SO₄ rejection (98.97%). The amide bonds formed between S-CONs and TMC also improve chlorine resistance. This demonstrates the potential of functionalized 2D CONs for efficient NF membrane modification.