Constructing an efficient catalytic layer through the design of catalyst structures is an effective way to reduce sustainably platinum loading for proton exchange membrane fuel cells (PEMFCs). Herein, we report a three-dimensional model of an order-structured cathode catalyst layer (CCL) under the water flooding condition, which uses vertically aligned carbon nanotubes (VACNTs) as the catalyst support with an ultralow Pt loading of less than 0.1 mg cm −2 to optimize the structure of such an electrode and explore the possibility to achieve the U.S. Department of Energy (DOE) 2020 target. The model effectiveness is validated by comparing it to a single practical fuel cell with the Pt loading of 0.035 mg cm −2 at the cathode side. Meanwhile, parametric studies including the length and spacing of VACNTs and the Nafion thickness are carried out to optimize the order-structured CCL. The results demonstrate that the VACNT-based CCL has excellent performance even under the water flooding condition due to its fast reaction characteristics, and by optimization of the electrode structure, the current density of the optimized CCL can be increased by 26% at the cathode potential of 0.8 V and the current density can be increased by 84% at 0.75 V, compared to that of the practical VACNT CCL. Furthermore, the DOE 2020 targets can be fulfilled with feasible CCL parameter adjustment including the radius of VACNTs, the catalyst surface area per unit mass, the flooding condition, and the Pt loading, which make the orderstructured electrode a very promising candidate to enhance the development of PEMFCs with an ultralow Pt loading.