An active micro-mixer equipped with an oscillating stirrer is considered by analyzing the mixing behaviors, i.e. the effect of the Karman vortex, the flow structure after the stirrer, etc. The mixing was calculated by the D2Q9 model of Lattice Boltzmann methods. In this study, the time– averaged mixing index formula, I D , is newly proposed for time dependent flow. Three models are tested and the mixing indices are compared. From the results, it was found that the mixing of Model III is enhanced and stabilized much more than the other models. Therefore, an optimum design for a dynamic micro-mixer with an oscillating stirrer was performed. The design variables were established as the length, the angle and frequency of the stirrer. It is found that the optimal design variables are determined by 0.66, 107.9 o and 0.49 Hz.