This study investigates electrospun polyvinyl chloride/thermoplastic polyurethane (PVC/TPU) nanocomposite membranes embedded with 0, 0.05, 0.10, and 0.15 wt% functionalized multi-walled carbon nanotubes (fMWCNTs). The fMWCNTs were thermally treated and functionalized to improve dispersion and interfacial adhesion. SEM analysis revealed uniform nanofibers with diameters of 70–85 nm and no bead defects. FTIR confirmed the presence of hydrophilic functional groups on fMWCNTs. Mechanical tests showed a substantial increase in elastic modulus from 30 MPa (pristine membrane) to 334 MPa with 0.15 wt% fMWCNTs. Water contact angle decreased from 127° to 68°, indicating enhanced hydrophilicity and improved wettability of the electrospun membranes incorporated with fMWCNTs. Permeation experiments using humic acid (HA) as a model pollutant demonstrated high water flux: 551 L.m− 2.h− 1 for pure water and 388 L.m− 2.h− 1 for HA solution with the 0.15 wt% fMWCNT membrane. This membrane also achieved over 99% HA rejection and a low irreversible fouling ratio (6.7%) after 240 min, highlighting excellent antifouling performance. The incorporation of fMWCNTs significantly enhances mechanical strength, hydrophilicity, permeability, fouling resistance, and performance stability of the membranes. These results indicate that PVC/TPU/fMWCNT nanofiber membranes are highly promising for efficient removal of organic pollutants in wastewater treatment applications.