Biological proton pumps ferry protons in an active manner and have a high flux (a few to 10 protons/(s·nm²)). Integrating these features in an artificial membrane may open the way for a wide range of applications but it remains challenging. In this work, we employed a structural engineering strategy to construct an asymmetric photonic polymeric carbon nitride (C₃N₄) membrane that exhibited photo-driven high flux proton pumping performance. The ion transport path through the membrane is reminiscent of that in the high-flux asymmetric biological ion channel. In addition, it has a photonic structure that mimics the mosquito compound eyes with improved light adsorption. Finally, the asymmetric structure constitutes an isotype (n–n) heterojunction that enhances the separation of the light-induced electron–hole pairs. As a result, the membrane shows a flux of 89 μA/cm² under 100 mW/cm² white light illumination (approximately one sun), the highest ever reported. This translates to a pumping rate of ~ 6 proton/(s·nm²), comparable to the biological counterpart. This work highlights the potential of multi-level structural engineering to construct high-performance bionic devices, and may find applications in solar energy harvesting and solar powered membrane process.