The electrochemically mediated amine regeneration (EMAR) carbon dioxide (CO2) capture process has significant potential in mitigating CO2 emissions. A suitable desorption reactor plays a pivotal role in realizing the efficient utilization of the EMAR technology. This study concentrates on the simulation and improvement of the desorption reactor for the EMAR process. To begin with, a comprehensive multi-physics model was developed to simulate the desorption process within a laboratory flat-plate reactor. The concentration distributions of reactive ions and the effect of CO2 bubbles in the electrolyte were analyzed. Results indicated that shortening electrode length is a practical measure to enhance desorption reactor efficiency. The study also explored the impact of critical operational variables, including electrolyte flow direction, flow rate, copper ions loading, and applied potential. Notably, controlling the applied potential proved highly effective for regulating desorption performance, with optimal adjustment maximizing overall efficiency. Based on these findings and the characteristics of the EMAR process, a novel multi-electrode partitioned EMAR desorption reactor was proposed as an enhancement to the flat-plate reactor. By applying distributed potential, improved desorption performance was obtained, resulting in a 20.05% increase in the CO2 desorption rate with only a 4.04% increase in the unit desorption energy consumption. These findings provide significant insights for optimizing the design and implementation of the EMAR desorption reactor.