An electric double layer (EDL) generally exists at the interface between a conductive electrode and its adjacent liquid electrolyte. Accurate measurement of the capacitance of EDL is requisite but a great challenge due to the complexity of its variation mechanism correlated with the magnitude and frequency of applied signals and the difficulty in measuring the inner layer potentials across the EDL. Herein, a novel dielectrophoresis (DEP)-based approach is proposed to measure the capacitance of an EDL at a microelectrode/electrolyte interface. The measurement is achieved by employing DEP manipulation to micro polystyrene (PS) spheres suspended in a liquid electrolyte and determining the capacitance of EDL on the microelectrodes from the moving velocities of spheres. This method allows measurement of the capacitances of EDL under alternating current (AC) signals with different magnitudes and frequencies, so that the capacitance change with the magnitude and frequency of the applied signal can be characterized. The method avoids the impedance interference from the liquid electrolyte, external measuring systems, and other crosstalks, enabling an accurate measurement of double layer capacitance. In addition, the inner layer potentials across EDL under different magnitudes and frequencies of applied signals are comprehensively investigated, which facilitates an understanding of the ion behavior at the interfacial boundary that governs external observations of electrochemical reactions. The accurate measurement of the capacitance of EDL is of significance to explore the mechanism of interfacial functioning of electrochemical and bioelectrical devices and systems.