Typically commercial controllers do not give data of the controller gains. Therefore, it is very hard to determine the optimal controller gain even though the dynamic model is derived. In this case, design of experiment (DOE) methodology can be a powerful tool for gain tuning. In this research, gain tuning process is proposed based on the DOE. Micro parallel mechanism platform with 3 degrees-of-freedom (DOF) is used for the experiments. Controller gains are measured indirectly from the voltages of adjustable resistors. The controller gains of three actuators are optimized by two or three steps, respectively. The correlations of the controller gains are also analyzed. The process and methodology can be adopted in gain tuning of other mechanical systems.