In this study, we studied the fabrication of a cation-exchange membrane (CEM) with high permselectivity for monovalent ions that can be applied to an electrodialysis (ED) process for efficient separation of acid-metal ions from acid wastewater. The pore-filled cation-exchange membranes (PFCEMs) were fabricated by filling a porous substrate with sodium 4-vinylbenzenesulfonate (NaSS) monomers having sulfonic acid groups and vinylphosphonic acid (VPA) monomers having phosphonic acid groups together with a crosslinker into an asymmetric structure and in-situ photopolymerization. The fabricated PFCEMs had a slightly lower ion-exchange capacity than that of a commercial membrane, but they exhibited electrical resistance and mechanical properties suitable for practical applications. The permselectivity of the PFCEMs fabricated with various NaSS:VPA molar ratios and a commercial membrane (CSE, Astom, Japan) in H+/Fe2+ mixed solutions was measured. The best permselectivity was confirmed at the condition of NaSS:VPA = 25:75, which was more than 10 higher than that of the commercial membrane. In addition, the ED results of H+/Fe2+ mixed solution using the optimally fabricated membrane showed excellent acid-metal ion separation performance compared to the commercial membrane. The CEM including both sulfonic acid groups with excellent ion conductivity and phosphonic acid groups with strong binding affinity for metal ions is expected to be effective in separating various valuable metal ions in addition to Fe2+ from acid waste solutions.