The microchip-based electrochemical detection system (μEDS) has attracted plenty of research attention due to its merits including the capability in high-density integration, high sensitivity, fast analysis time, and reduced reagent consumption. The miniaturized working electrode is usually regarded as the core component of the μEDS, since its characteristic directly determines the performance of the whole system. Compared with the microelectrodes with conventional shapes such as the band, ring and disk, the three-dimensional (3D) micropillar array electrode (μAE) has demonstrated significant potential in improving the current response and decreasing the limits of detection due to its much larger reaction area. In this study, the numerical simulation method was used to investigate the performance of the μEDS, and both the geometrical and hydrodynamic parameters, including the micropillars shape, height, arrangement form and the flow rate of the reactant solution, were taken into consideration. The tail effect in μAEs was also quantitatively analyzed based on a pre-defined parameter of the current density ratio. In addition, a PDMS-based 3D μAE was fabricated and integrated into the microchannel for the electrochemical detection. The experiments of cyclic voltammetry (CV) and chronoamperometry (CA) were conducted, and a good agreement was found between the experimental and simulation results. This study would be instructive for the configuration and parameters design of the μEDS, and the presented method can be adopted to analyze and optimize the performance of nanochip-based electrochemical detection system (nEDS).