In this study, a well-shaped microelectrode array (MEA) for fabricating a high-density complementary metal-oxide semiconductor amperometric electrochemical sensor array was designed and verified. By integrating an auxiliary electrode with the well-shaped structure of the MEA, the footprint was reduced and high density and high resolution were also achieved. The results of three-dimensional electrochemical simulations confirmed the effectiveness of the proposed MEA structure and possibility of increasing the density to four times than that achieved by the conventional two-dimensional structure.