The working environment of fuel cell is changing, so the physical states (temperature, humidity, pressure, etc.), electronic load, heat load and ambient conditions of the fuel will affect the work of fuel cell, so test analyzer control software must be able to judge the accuracy of external measurement and system failures. In other words, it has self-diagnosis function. The control software must also be able to automatically adjust the control strategy according to the working environment and performance. The core of the control system software is parameters tuning which is found on separate integral PID control algorithm [3][4].Control system analyzes the data of the sensors, and then regulate controlled variable under the control of control results, and deal with potential failures in accordance with the preset results of the system to achieve the optimization of system control.