The performance of polyamide-based thin film nanocomposite (TFN) membranes essentially hinges on nanofillers, polyamide (PA) selective layer and the interaction between them. Incorporating synthesized nanofillers into PA layer has attracted significant attention, yet this fabrication route suffers from the unsatisfactory interfacial compatibility between nanofillers and polymer matrix. As pure organic nanofillers, covalent organic frameworks (COFs), however, are constrained by their large pore size and demanding synthesis condition. Herein, COF TpHz was synchronously synthesized with the interfacial polymerization (IP) process of PA layer to fabricate COFs incorporated TFN membranes. The addition of TpHz was optimized by controlling the content of monomers and the resultant TFN membrane achieved enhanced nanofiltration performance thanks to the in-situ synthesized TpHz. At ambient temperature, the prepared membrane showed higher permeance (23.6 L m 2 h −1 bar −1 ) and salt rejection (96.9%) than the pristine thin film composite (TFC) membrane under 4 bar toward 1 g/L Na 2 SO 4 solution, corresponding to an improvement of 44.8% and 3.2% of permeance and rejection, respectively. Meanwhile, the anti-fouling property of the prepared membrane was also improved compared with TFC membrane. This in-situ interfacial polymerization (IIP) strategy proposes a new idea for the preparation of COFs incorporated TFN membranes, revealing its promising prospect in desalination. • Synchronization formation strategy on the polyamide and covalent organic frameworks (COFs) is proposed. • COFs were in-situ synthesized under a mild condition and characterized by visualized method. • The resultant novel membrane exhibited high water permeance (23.6 L m −2 h −1 bar −1 ) and Na 2 SO 4 rejection (96.9%). • The combined effect of polyamide and multi-layer COFs on desalination performance is discussed.