Summary: Thin film membranes of covalent organic frameworks are promising for high-permeance molecular separation. However, their synthesis needs a high temperature or longer reaction time, unsuitable for large-scale fabrication of thin film composite membranes. The ultrathin film of porous organic polymers as a separation layer of the composite membrane could be a close alternative to COF membranes. Here we report transition metal ion-catalyzed room temperature fabrication of the ultrathin (≈12 nm) polyimine nanofilms via interfacial polymerization of melamine and triformylphloroglucinol onto hydrolyzed polyacrylonitrile support within a short reaction time. Composite membranes exhibit high water permeance (≈78 L m−2 h−1 bar−1), high rejection (99.6%) of brilliant blue R (825.9 g mol−1), low rejection of NaCl (≈1.8%) and Na2SO4 (≈17%), and enable efficient molecular separation. The role of metal ion catalysts for large-area fabrication of the ultrathin polyimine nanofilm membranes used for molecular separation is demonstrated.