Designing and preparing nanofiltration (NF) membrane with distinguished property of acidic tolerance is attractive for handling acidic saline wastewater. In this work, we used a new monomer of 2,2-bis(3-amino-4-hydroxyphenyl)-hexafluoro-propane (bisAPAF) to prepare NF membrane by interfacial polymerization for removing dyes from acidic saline solution. Interestingly, the resulted NF membrane derived from bisAPAF and 1,3,5-trimesyol chloride (TMC) exhibits an exceptional structure stability under strong acid condition. Specifically, after exposed to H2SO4 aqueous solution with concentration of 20% (w/v) for 720 h, the NF maintains a Na2SO4 rejection of ∼87%, showing little change as compared with the membrane without acidic treatment. In addition, the membrane shows a high selectivity for differentiating Direct Red 23/NaCl or Congo Red/NaCl in the pH range of 2–9, the rejection of dyes maintains at higher than 98% while the NaCl rejection is lower that ∼10%. The outstanding acid tolerance property of NF membrane makes it a great promise candidate for acid wastewater remediation.