Abstract: The intractable trade-off between proton conductivity and vanadium ion selectivity, known as the ‘transmission paradox’ is a critical bottleneck hindering the commercialization of vanadium flow batteries (VFBs). Inspired by the multi-stage, synergistic filtration mechanism of the mammalian glomerular filtration barrier, a novel, biomimetic hierarchical composite membrane has been fabricated via a precise layer-by-layer strategy on a polyethylene (PE) substrate. This membrane integrates a polydopamine (PDA) adhesion layer, a sulfonated Zr-MOF ion-sieving layer, and a synergistic polybenzimidazole (PBI) matrix. Spectroscopic analysis confirmed the formation of a critical bifunctional acid–base interface (–SO₃⁻···H⁺N–) between the MOF and PBI, which densifies the structure and optimizes ion pathways. The resulting composite membrane exhibits excellent mechanical robustness, superior chemical stability, and exceptional dimensional stability. Most significantly, this architecture successfully decouples the performance trade-off, demonstrating both high proton conductivity (11.11 mS·cm⁻¹) and remarkably suppressed vanadium ion permeability (2.4 × 10⁻⁸ cm²·min⁻¹). This combination yields an outstanding ion selectivity of 46.29 × 10⁴ S·min·cm⁻³. When tested in a VFB single cell, the membrane enabled a high energy efficiency of 81.6% at 200 mA·cm⁻², an ultra-long self-discharge time of 2700 min, and excellent long-term cycling stability. This biomimetic design strategy effectively resolves the core ‘transmission paradox’ offering a promising pathway for next-generation high-performance flow batteries.