Digital microfluidics (DMF) is a promising lab-on-a-chip technology which has been applied in a wide variety of fields, including chemical sensing, biological detection, and even mechanical transportation. However, the appearance and functions of current DMF have been limited within two-dimensional planar space because of the conventional fabrication methods, such as photolithography or screen printing. In this paper, we report a DMF system which utilizes the advantage of three-dimensional (3D) printing to develop the novel form factor of electrodes and conversion of channels from planar to 3D forms. Vertical channels have been fabricated through combined 3D printing methods to facilitate stable and controlled movement of water droplets. The interfaces among liquid, gas, and solid were analyzed through Young-Lippmann law. We calculated the actuation force in a series of different configurations to enable us to optimize the system. Inspired by xylem structures in plants, the vertical movement and pumping of droplets are demonstrated by a programmable control system with a built-in boost converter for a real-time operating and portable DMF system. This work validates the promise of 3D printing to make 3D vertical DMF devices and the potential of the artificial xylem chip for micropumping applications.