The high voltage cascaded charging power supply is applied to the electromagnetic lunch system as the prime energy. A control system based on the time sequence code control strategy is designed to control the opening time of 20 cascaded battery modules during charging. The charging voltage can be regulated from 0 to 10 kV, with high accuracy, controllable current, and the ability to cycle charge. The architecture of MCU and FPGA is adopted in the hardware circuit of the control system, and ARM is used as the main control chip. High-speed optic-electric converter devices and optical fibers are used as trigger signal transmission systems to increase anti-interference ability. The upper computer software is designed to set parameters such as time sequence of each cascaded module, charging voltage, and cycle charging times. Some experiments are conducted to verify the performance of the this control system, which obtain good charging waves consistent with the design.