Numerical investigation of 3D electrokinetic mixing through micromixer has performed both qualitatively and quantitatively. In order to reduce numerical expenses of 3D flows, we implement the Helmholtz-Smoluchowski method for the numerical modeling of electroosmotic flows. According to the previous study of electrokinetic mixing inside the heterogeneous microchannels, existence of the vortexes within the flow field always increase the mixing performance for 2D flows. However, investigations of 3D micromixers show that this increase does not happen for all the situations and in some cases, existence of the vortexes does not enhance the mixing performance. Findings of this research indicate that the asymmetry degree of the flow field pattern is the key parameter for the mixing performance. Within the 3D flow field, there are more opportunities to increase the asymmetries. Consequently, mixing performances of the 3D flows are much larger compared to those of 2D flows. Studies of various 3D cases for electroosmotic micromixer show that mixing performance can be improved or deteriorated depending on the arrangement of the heterogeneities over the microchannel walls. These results confirmed that 2D simulation of mixing could not explain the complete benefits of passive micromixers. These results can apply to the simulation of micromixers used in Lab-on-a-chip devises.