A novel design of the dual-layered catalyst layer is performed using catalytic layers with different degrees of phase separation of Nafion. Empirical equations of the water uptake and the proton conductivity are introduced for highly phase-separated catalyst layer. Simulation results are in good agreement with experimental data using catalyst layers prepared from different solvents, which are carefully designed to have different degrees of phase separation. The effect of highly phase-separated catalyst layer is further investigated with different electrode configurations. As a result, the highly phase-separated catalyst layer shows promising aspects as an efficient water protective layer with catalytic activity. Consequently, the proposed electrode, composed of a highly phase-separated external layer and a lowly phase-separated inner layer, results in an increase of the cell performance in the high-current region.