Studying electrophysiological properties of cells helps us to further understand the origin of the disease. However, the electrical signals of cells are weak and difficult to measure accurately. In this work, we analyzed the effects of the cleft thickness (d), the height of the microelectrode (h) and the radius of the microelectrode (r) on the sealing resistance, and designed an analog electronic circuit of the 3D microelectrode array engulfed by a myocardial cell for studying the effects of microelectrode size r and h on the cell signal. The method of microelectrodes optimisation is obtained through the simulation of electrical signals collected by varying size microelectrodes, which provides a design idea for optimizing the size of microelectrode arrays.