Membranes with precise control of selective layer are designed and prepared by adjusting diffusion of solvents. Combining experiments and theoretical calculations, the formation mechanism of ion conductive membranes prepared by a non‐solvent induced phase separation (NIPS) method is found to be related to internal diffusion flux of solvent to the non‐solvent bath and external diffusion flux of non‐solvent to the casting solution. By regulating the internal and external diffusion rates via a two‐step NIPS method, a series of polybenzimidazole (PBI) porous membranes with independently controlled thin selective skin layers and highly porous support layers are fabricated, which achieve a simultaneous improvement in ion selectivity and proton conductivity. A vanadium flow battery assembled with a PBI membrane demonstrates an energy efficiency of 80% at a current density of 220 mA cm−2, which is the highest value among the reported PBI membranes. This provides a simple and effective way to fabricate membranes with well‐defined morphologies.