Rising freshwater scarcity in arid regions requires advanced desalination and resource recovery technologies to address brackish water threats to agriculture, drinking water, and ecosystems. Charge-asymmetric Janus nanofiltration (NF) membranes demonstrate significant potential for resource recovery in brackish water treatment, particularly enabling efficient ion-selective separation. However, current models remain limited to qualitative speculation regarding the ion transport mechanisms in Janus membranes, as they fail to incorporate quantitative descriptions of axial charge heterogeneity. Herein, we address this gap by integrating axial charge distribution into the Donnan steric pore model with dielectric exclusion (DSPM-DE). A charge-asymmetric Janus membrane (R90-AC) was fabricated by coating a positively charged polyelectrolyte layer onto a commercial NF membrane (R90-SC). The axial-charge-distributed DSPM-DE model reduced prediction deviations for six ions in brackish water systems to < 8%, outperforming conventional models (deviations > 16%). Theoretical simulations revealed an intrinsic electric field (18.87 mV·μm⁻¹) within Janus structures, driving anomalous electromigration contributions exceeding 100% for cations and −50% to −20% for anions. This “electrostatic diode” effect was experimentally validated, with Mg²⁺ forward flux (2.69 × 10⁻² mol·m⁻²·h⁻¹) surpassing reverse flux (2.98 × 10⁻³ mol·m⁻²·h⁻¹) by nearly an order of magnitude. The study bridges theoretical modeling and practical structure design, offering a robust framework for tailoring charge-asymmetric structures in ion-selective separations.