The invention discloses a method for preparing a modified composite nanofiltration membrane by constructing a pure COFs intermediate layer, which mainly includes: preparing TpPa-1 by using Schiff base condensation, constructing a pure COFs intermediate layer on a porous base membrane by vacuum filtration, and then A composite nanofiltration membrane is obtained through interfacial polymerization, wherein the porous base membrane is a polymer porous membrane with a pore diameter of 0.1 μm. In the present invention, by controlling the concentration of the aqueous phase monomer and the organic phase monomer in the interfacial polymerization step and the drying time after the interfacial polymerization reaction ends, the internal pore moisture and piperazine of the formed composite nanofiltration membrane can be effectively controlled. Molecules, that is, the hydrophilicity and porosity of the polyethersulfone-based membrane surface are optimized by vacuum filtration of the hydrophilic COFs intermediate layer, thereby realizing precise regulation of the interfacial polymerization process. The polyamide separation layer prepared by this method is thin and dense, Under the lower operating pressure (0.2MPa), it has higher water flux and maintains excellent separation performance.