The flat-top high magnetic field (FTHMF) can meet the demands of some scientific experiments for the extreme environment with strong electromagnetic characteristics. Therefore, the FTHMF has become a vital research tool in physics, chemistry, and biology in recent years. The multiple-capacitor power supply (MCPS) consists of multiple capacitor modules output high voltage. Currently, an FTHMF with a single-coil magnet energized by the MCPS is achieved at Wuhan National High Magnet Field Center. To further improve the magnetic field strength and stability, this paper proposes an FTHMF system powered by two MCPSs with a dual-coil magnet. The operating characteristics of the system in the dual-coil case are analyzed, and an evolutionary algorithm obtains the parameters of the dual-coil magnet. The models of the designed system are built in MATLAB/Simulink and COMSOL Multiphysics to verify the effectiveness of the design method.