The Polymer Electrolyte Membrane Fuel Cell (PEMFC) system is considered as one of the most potential power plant on vehicle. However, the efficiency of the high power fuel cell stack has restricted the high power system which is developed for the full power fuel cell vehicle. The multi-stack system integrated by several fuel cell stacks is a solution aimed for high power level system. However, the inconsistency of the stacks flow distribution restricts the performance uniformity of each stacks and the efficiency of the multi-stack fuel cell system. In this paper, a dual-stack polymer electrolyte membrane fuel cell system was setup, and its intake manifold was established. A porous medium was applied to replace the complex flow field structure inside the fuel cells to simulate the pressure drop of the gas through the stack. According to the operating conditions of the vehicle, variable conditions are designed to carry out simulation experiments for the first time. The results show that there is not a significant effect of the changing load's range on the instantaneous uniformity. However, the initial value of the changing load has a great influence on the instantaneous uniformity. In addition, the settling time of the loading process is much shorter than that of the load shedding process. The equivalent model of porous media proposed provides a new method to model the fuel cell stack, which is very useful in the fuel cell pipe system design and system dynamic response analysis. The uniformity simulation result provides the directions for the fuel cell control strategy design and optimization, and the references for gas intake manifold design.