O-Polar ZnO(0001) single crystals and ZnO and Mg-doped ZnO (MgZnO) films which were subsequently deposited on the ZnO crystals by a pulsed laser deposition (PLD) method were electrochemically investigated through the interfaces with ionic liquid (IL) in a vacuum. The sample surfaces were confirmed to be atomically clean and flat by reflection high energy electron diffraction (RHEED) observation, prior to their electrochemical measurements. Electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) were then performed, and the donor density, flat band potential of these ZnO samples, and the electric double layer capacitance at the IL/ZnO interfaces were successfully evaluated. The flat band potentials of ZnO and MgZnO films were found to shift to more negative potentials relative to those of the single crystal ZnO, with different values for thicker films, respectively. Some possible origins of the different flat band potentials between ZnO and MgZnO films, and their film thickness dependence of the flat band potential will be discussed in this paper.