We propose a 3D microfluidic mixer based on the alternating current electrothermal (ACET) flow. The ACET vortex is produced by 3D electrodes embedded in the sidewall of the microchannel and is used to stir the fluidic sample throughout the entire channel depth. An optimized geometrical structure of the proposed 3D micromixer device is obtained based on the enhanced theoretical model of ACET flow and natural convection. We quantitatively analyze the flow field driven by the ACET, and a pattern of electrothermal microvortex is visualized by the micro-particle imaging velocimetry. Then, the mixing experiment is conducted using dye solutions with varying solution conductivities. Mixing efficiency can exceed 90% for electrolytes with 0.2 S/m (1 S/m) when the flow rate is 0.364 L/min (0.728 L/min) and the imposed peak-to-peak voltage is 52.5 V (35 V). A critical analysis of our micromixer in comparison with different mixer designs using a comparative mixing index is also performed. The ACET micromixer embedded with sidewall 3D electrodes can achieve a highly effective mixing performance and can generate high throughput in the continuous-flow condition.