Nanofiltration membranes with high charge density are highly attractive for selectively removing organic micropollutants and divalent anions from water environments. Here we constructed polyamide (PA) membranes with ultra-high negative charge density via a sea-squirt nanofibrillated cellulose restricted interfacial polymerization process. Sea-squirt nanofibrillated cellulose, which contains a high content of 7.0% carboxyl groups and 29.8% hydroxyl groups, effectively fettered piperazine and regulated the interfacial polymerization reaction kinetics. As a result, the optimized membrane had an ultra-high zeta potential of −148 mV at pH 7 and a charge density of −32.6 mC m⁻². This membrane achieved outstanding performance metrics, including a water permeance of 41.5 l m⁻² h⁻¹ bar⁻¹, exceptional SO₄ ²⁻/Cl⁻ selectivity of 144.5 and greatly increased water/organic micropollutant selectivity. Molecular dynamics simulations revealed a 73.1% reduction in the diffusion rate of piperazine due to competitive forces, leading to a PA surface enriched with -COOH groups. This work provides an effective strategy for tuning the PA membrane charge density to increase water purification and wastewater treatment efficiency.