Incorporating hydrophilic and charged porous nanofillers to prepare high-performance thin film nanocomposite (TFN) nanofiltration (NF) membranes is an effective method to achieve efficient water treatment. In this study, we synthesize the sulfonated covalent organic framework nanosheets (S-CONs) with higher hydrophilicity and electronegativity by immobilizing sulfonic acid groups (–SO3H) on TpPa-1 nanosheets. The S-CONs are incorporated in the PA layer by interfacial polymerization (IP) reaction. The results indicated that the S-CONs could modulate the hydrophilicity, thickness, and electronegativity of TFN-NF membranes. At the optimal addition of S-CONs (0.006 g), the pure water permeance increases to 8.84 L⋅m−2⋅h−1⋅bar−1\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\\rm{L}}\\cdot{\\rm{m}}^{-2}\\cdot{\\rm{h}}^{-1}\\cdot{\\rm{bar}}^{-1}$$\\end{document}, which is about 1.75 times than the TFC membrane, with a high Na2SO4 rejection reaching 98.97%. The improvement of the separation performance mainly results from the reduction of PA layer thickness (from ~178.00–198.00 to ~100.00–128.00 nm) and the increase of surface electronegativity (from −20.37 to −44.41 mV at pH = 7.00). More interestingly, the amide bond formed between the S-CONs and TMC improved the chlorine resistance of the membranes. This study reveals the potential of using functionalized 2D CONs as nanofillers to modify TFC membranes for efficient nanofiltration.