This work provides a novel three-dimensional numerical analysis of electrokinetic mixing in microflows with different electrical conductivities. Our study examines ferrofluid and water co-flow mixing quantitatively, which has been overlooked in previous micromixers based on electrokinetic instabilities. This has become possible by considering the actual diffusivity of ferrofluid. The findings reveal that thinner channels exhibit stronger suppression of instability due to the pronounced effect of walls on the flow, emphasizing the importance of 3D simulation for shallow channels. Additionally, increasing the electric field intensity was found to have dual opposing effects on instabilities and electrolyte mixing. It enhances the body force and instabilities, improving mixing, but also accelerates flow velocity, reducing fluid residence time and leading to weaker mixing of the flows. A notable observation was a decrease in the mixing index with the augmentation of electric field intensity; for a channel with H = 200 µm, the mixing index reduced by approximately 13% when the electric field strength was increased from 179 to 210 V/cm.