Traditional nanofiltration membranes face challenges such as membrane fouling and difficulties in achieving precise separation of small organic molecules. A promising solution to these issues is the preparation of thin-film nanocomposite membranes. In this study, Cu and Ag bimetals were incorporated into covalent organic frameworks to fabricate thin-film nanocomposite membranes. The hydrophilic monomer 1,3,5-tris(4-aminophenyl) benzene of covalent organic frameworks was introduced as a water phase monomer during interfacial polymerization to enhance the organic–inorganic compatibility. The incorporated covalent organic frameworks within the thin-film nanocomposite membrane loosened the selective layer, resulting in an enhanced permeability of 24.6 LMH bar⁻¹. The membrane exhibited a rejection rate over 99.0% for Congo Red, Xylene Brilliant Cyanine G, and Reactive Blue, while exhibiting relatively low rejection rates of MgCl₂ and NaCl. Moreover, the outstanding catalytic capability of the incorporated bimetals led to a 4-nitrophenol conversion rate of 84.38%, enabling simultaneous conversion and separation. The integration of covalent organic frameworks and bimetals also imparted robust antibacterial properties, significantly enhancing operational stability. In conclusion, the covalent organic framework-Cu/Ag-based thin-film nanocomposite membrane demonstrated superior catalytic and separation capabilities, presenting a promising alternative for advanced filtration applications.