A pixel unit structure, as well as a manufacturing method thereof, is provided. The pixel unit structure includes a display medium module and an active switching element. The display medium module includes a first electrode, a second electrode and a display medium. The first electrode and the second electrode are separated from each other, and the display medium is disposed between the first electrode and the second electrode. The active switching element is electrically connected to the first electrode, for allowing the first electrode and the second electrode to change the state of the display medium. The active switching element includes a wafer portion and a transistor portion, which is formed on the wafer portion. Therefore, the active switching element can be manufactured independently without the restriction from the display medium module.