A greater understanding of the dynamic processes inside the stack is urgently needed to optimize the PEMFC (proton exchange membrane fuel cell). In this study, we examined the gas, water and electrochemical processes inside the stack, studied the physical dynamics of system accessories such as gas supplement, flow and pressure-regulating devices, then used Simulink to build a mathematical model of a complete PEMFC system; a segmented testing platform was built to test the spatial distribution of RH (relative humidity) and pressure, which was used to verify the simulation model; based on this model, the complicated phenomena occurring inside the stack during fluctuating operating states were calculated. Our findings showed that the pressure in the gas channel and exhaust manifolds decreased when the external load increased, changing sharply at the moment of load change. The transient pressure difference between the cathode and anode sides (several kPa) had a huge impact on the MEA (membrane electrode assembly); when the load current increased, RH in cathode and cathode channel increased gradually, and the increasing rate of anode side was bigger than that in cathode side. The influence of variance magnitude and change interval of external load were also studied based on the model.