Carbon nanofibers (CaNFs) exhibit promising applications in the fields of environmental science and nanotechnology, and self-assembled peptide nanofibers (PNFs) are useful for the biomimetic synthesis of organic-inorganic hybrid nanomaterials and the fabrication of functional hybrid membranes for the removal of various pollutants from water. In this work, we report the biomimetic synthesis of hybrid nanomaterials by the interweaving of CaNFs and PNFs. Using the biomimetic mineralization properties of PNFs, ZrO2 nanoparticles were synthesized along the nanofiber surface, and then functional nanohybrid porous membranes were prepared by the vacuum filtration technology. For the fabrication of membranes, the amount of PNFs and ZrO2 precursors in the hybrid membrane were optimized. The designed organic-inorganic hybrid membranes exhibited high removal performance for fluorine ion (F−) from water, and the removal efficiency of the fabricated membranes towards F− ion-containing aqueous solution with a concentration of 50–100 mg/L reached more than 80%. In addition, the nanofiltration membranes revealed good adsorption capacity for F− ions. It is expected that the strategies shown in this study will be beneficial for the design, biomimetic synthesis, and fabrication of nanoporous membranes for economic, rapid, and efficient water purification.