A hybrid capacitor-battery power supply is built at Wuhan National High Magnetic Field Center to generate a steep rising/flat top waveform, where the capacitor banks provide the sharp rising edge and the batteries maintain the flat top long pulse. A control system, which consists of a global controller and subcontrol system, is designed to ensure the reliable operation. The global controller includes a triggering unit, an interlock unit, and a data transmission unit. Each type of power source can be discharged separately through its own subcontrol system. When different powers discharge together, its own control system fulfills internal operations, and the triggering unit is responsible for generating the highest priority triggering signals, the interlock unit is applied for protecting multitype power modules. The data transmission unit is used to communicate with different power modules. Based on the designed control system, the operation strategy and reliability analysis are discussed. The result shows that the control system could greatly improve the performance of the hybrid capacitor-battery power supply.