The invention discloses a super-hydrophobic single-plate digital micro-droplet transport device, and a manufacturing method thereof. The super-hydrophobic single-plate digital micro-droplet transport device comprises, from the bottom to the top, a substrate, electrodes, a medium layer, and a super-hydrophobic layer successively; the substrate is a glass or Si substrate; the electrodes are ITO glass electrodes, Au / Cr(Au / Ti) or Al / Cr(Al / Ti) thin film electrodes; and the super-hydrophobic layer is made of boron nitride nanotubes. The manufacturing method comprises following steps: step 1, the substrate is cleaned; step 2, the substrate is provided with the electrodes; step 3, the electrodes are provided with the medium layer via deposition; and step 4, the medium layer is coated with the boron nitride nanotube super-hydrophobic layer via spin coating. Advantages of the super-hydrophobic single-plate digital micro-droplet transport device are that: digital micro-fluidic chips are prepared via micro mechanical processing technology, structure is simple, operation is convenient, and it is beneficial for expansion of subsequent functions. The super-hydrophobic single-plate digital micro-droplet transport device is capable of reducing waste of precious samples, reducing driving voltage, maintaining biological activity of samples, increasing feasibility and practicality of experiments, and promoting smooth implementation of experiments of the bio-medical field; and integration with IC, and achieving of more functions are convenient.