Abstract: With the advantages of low noise, low infrared signature and high dependability, the fuel cells can be used for the military vehicles and field power supply. The reaction characteristics of proton exchange membrane fuel cell (PEMFC) system are affected by selfconfiguration, environment and other factors. For the limit of sensor technology, the inner temperature and humidity of the fuel system can’t be measured immediately, and its reaction characteristics are different every time. System model is difficult to build, its inner humidity can’t be well controlled using a traditional control method. For 3 kW PEMFC system, a simple control system was built to control the humidity dynamically, which keeps the humidity changing up and down alternately in dynamic threshold. The limit of system model is get rid of by this method, avoiding the humidity excursion caused by steadily control. Finally the feasibility of this control method was validated through experiment.