The substrate membrane plays a crucial role in determining the performance of composite nanofiltration membranes prepared by interfacial polymerization (IP). In this study, persistent hydrophilic modification of polyvinylidene fluoride-co-chlorotrifluoroethylene (PVDF-CTFE) was achieved by incorporating N-methylglucamine (N-MG) without altering the membrane's morphology or pore size. Moreover, thin-film nanofibrous composite (TFNC) nanofiltration membranes were prepared using the surfactant assembly regulated interfacial polymerization (SARIP) method with the modified PVDF-CTFE@N-MG nanofibrous membrane as the substrate. The effect of N-MG addition on the substrate membrane's hydrophilicity and the structure and performance of the polyamide (PA) separation layer was investigated. The results showed that the addition of N-MG significantly improved the hydrophilicity of the PVDF-CTFE nanofibrous membrane. The TFNC-5 membrane, prepared with the modified PVDF-CTFE@N-MG nanofibrous membrane as the substrate, exhibited permeability exceeding 13.5 L m−2 h−1·bar−1 for various dye solutions at 3 bar pressure, with rejection rates above 98 %. It also demonstrated excellent selective separation performance (separation factor for NaCl/Orange G reaching 97.38) and long-term operational stability. This work provides a method for the preparation of low-pressure, high-flux nanofiltration membranes, which is applicable to seawater desalination and dye wastewater treatment.