To minimize the internal polarization concentration (ICP) in FO process and improve the structural stability of thin film composite (TFC) forward osmosis (FO) membrane, a reactable hydrophilic nanofiber substrate was prepared by vacuum filtrating an interlayer composed of polydopamine nanoparticles (PDA NPs) onto an electrospun polyacrylonitrile nanofiber substrate. Then a TFC FO membrane with dense selective layer, low structure parameter, high water permeability and low salt permeability was prepared by the interfacial polymerization thereon. According to the T-peel test, the resulting TFC FO membrane showed greatly improved adhesion strength between selective layer and substrate due to the chemical bonding and entanglement between polyamides and the PDA NPs, and the strong adhesion between PDA NPs and the nanofibers. The ICP in FO process for the resulting membranes were minimized due to the application of the nanofiber substrates with low structure parameter (in the range of 290 ± 36 μm–354 ± 20 μm). These FO membranes performed well in the heavy metal ions contained water treatment, showed 1–2 times higher water flux (29.2 ± 0.3 L/m2h) compared with commercial TFC membrane (HTI-TFC) and high heavy metal ions rejection (99.5% ± 0.4%, 99.1% ± 0.5%, 98.1% ± 0.7% for Cr3+, Cu2+ and Ni2+, respectively) when using 2.0 M NaCl as draw solution. The findings provide the pathway for the design of nanofiber based FO membrane with improved structure stability and high performance by interfacial polymerization. Display omitted •PDA NPs composed interlayer was filtrated onto the nanofiber substrate.•TFC FO membrane was prepared on the PDA NPs modified nanofiber substrate.•Adhesion strength was greatly improved by using the PDA NPs modified substrate.•The ICP in FO process was minimized by using the prepared FO membrane.•The prepared FO membrane performed well in heavy metal ions removal.