A droplet propulsion system based on the electrowetting-on-dielectric (EWOD) is integrated in deep-trench microfluidic channels. Due to the unique three-dimensional multi-height silicon shadowmask, electrodes are simultaneously fabricated on the top, bottom and vertical walls of deep channels, thus enabling three-face EWOD driving by both the bottom and sidewalls. We have successfully moved a water droplet in a 230 mu m-deep, 750 mu m-wide trench by EWOD.