The powertrain of a fuel cell vehicle typically consists of two energy sources: a proton electrolyte membrane fuel cell (PEMFC) stack and a battery package. In this paper, multi-dimensional dynamic programming (MDDP) is used to solve the energy management strategy (EMS) of fuel cell hybrid powertrain. This study built a fuel cell hybrid powertrain model, in which the battery model is built based on the Thevenin equivalent circuit. In order to improve the calculating efficiency and maintain the accuracy of the algorithm, the state variables in each stage are divided into primary and secondary. In the reverse solution process, the corresponding relationship between the multi state variables grid and the optimal cumulative function has been changed from three-dimensional to two-dimensional. The EMS based on MDDP is applied to component sizing of a commercial vehicle. Simulations were conducted using MATLAB under the C-WTVC working condition. By analyzing the fuel economy and system durability, the optimal component combination of comprehensive performance is obtained. Compared with the EMS based on dynamic programming (DP), the proposed method effectively improves the calculation accuracy: the hydrogen consumption can be reduced by 3.10%, and the durability of the fuel cell and battery can be improved by 1.08% and 0.13%, respectively.