Electrode impedances are measured to quantitatively characterize the electrode-electrolyte or cell-electrode interfaces. In the case of high-density microelectrode arrays(MEAs) that have been developed for brainmachine interface applications, the characterization process becomes a repeating and time-consuming task; a system that can perform the measurement and analysis in an automated fashion with accuracy and speed is required. However, due to the large number of channels, parasitic capacitance and off-capacitance components of the switching system become the major factors that decreased the accuracy for the measurement of high impedance microelectrodes. Here we investigated the implementation of automatic impedance measurement system with analyzing the causes of possible measurement-related problems in multichannel switching configuration. Based on our multi-channel measurement circuit model, we suggest solutions to the problems and introduce a novel impedance measurement scheme using electro-mechanical relays. The implemented measurement system could measure |Z| < 700 $k{Omega}$ of impedance in - 10% errors, which can be widely applicable to high density neural recording MEAs.