Covalent organic framework (COF) has been recognized as a disruptive material for fabricating organic molecular sieve membranes. Acquiring crystalline and defect-free COF membranes directly on polymeric substrates is important for practical applications yet is highly challenging. In this study, a noncovalent complex (NCX) modulated fabrication of COF membrane on hydrolyzed polyacrylonitrile (HPAN) substrate via counter diffusion is proposed. The triaminoguanidine chloride-phytic acid noncovalent complex (Tg-PA NCX) is uniformly introduced onto the HPAN substrate, transferring the substrate into an ideal seeding layer and catalytic platform for COF nucleation and growth. Enhanced Tg monomer concentration derived from NCX enhance its concentration near the surface is observed, facilitating the heterogeneous nucleation for COF fabrication. In addition, the PA in the NCX acted as a catalyst, promoting the growth of the highly crystalline COF membrane afterward. The resulting TgTb/NCX/HPAN membrane shows a defect-free surface with high crystallinity. Also, it displays over 90% rejection to various dyes rejection rates (e.g., Evans blue, Methyl blue, Congo red, and Amido Black) and high solvent permeation for organic solvents (e.g., ethanol: 57.9 ± 2.1 L m-2h-1 bar-1, n-hexane: 215.0 ± 2.7 L m-2h-1 bar-1). This work holds great potential as a platform technology for fabricating high-performance organic molecular sieve membranes.