<p>The development of nanofiltration (NF) membranes is critical for achieving sustainable water purification and resource recovery. However, conventional polyamide NF membranes often encounter trade-offs between ion selectivity and water permeability. Herein, we introduce a dual-zwitterionic strategy by assembling zwitterionized polyethyleneimine (Z-PEI) and polyanionic phytic acid (PA) onto a polyamide substrate. This architecture enhances surface hydration and charge density, enabling synergistic ion exclusion through Donnan repulsion, steric hindrance, and metal-chelation mechanisms. The resulting M1-ZPEI-PA membrane achieved high removal efficiencies of more than 98% for heavy metal ions, including Zn²⁺, Cu²⁺, Pb²⁺, Cd²⁺, and Fe²⁺, as well as 58.93% removal of NaCl, while maintaining high water permeability. Classical all-atom Molecular Dynamics simulations performed to study the molecular structural properties and intermolecular interactions of M1-ZPEI-PA membrane with contaminants. This study offers a promising pathway toward high-performance NF membranes for sustainable water treatment and environmental remediation.</p>