A biomimetic aluminum oxide membrane having asymmetric channels with a minimum diameter of 20 nm, a maximum diameter of 80 nm, and a length of 5 µm was prepared using square pulse anodization. The membrane effectively permitted transfer of anions only and showed an ionic current rectification characteristic with a rectification ratio of 2.4. After the sulfonic acid group was introduced by surface modification, the membrane effectively permitted transfer of cations only and showed a rectification ratio of 2.7. This modulation of the ionic current rectification direction was consistent with the theoretical prediction through the numerical analysis of 2D models. These findings present a convenient method to control ion transport for the ion exchange membrane.