Abstract: In recent years, ion therapy technology has developed rapidly in China and abroad. To meet the demands of the accelerator commissioning and the energy requirements of the different treatment scheme for the accelerator facility, the power supplies of the dipole magnets in the energy selection and beam transport system are required to work in the modes of DC, in-order trigger and periodic pulse. Using the integrated box controller independently developed by the Institute of Modern Physics, Chinese Academy of Sciences, the control and protection function of the power supply are realized. In order to meet the requirements of commissioning and treatment working modes, the controller has been designed to support the local and remote control network protocols, between which the switch can be achieved through the button on the touch screen. The power supply specifications has been tested after the main circuit and controller were designed and assembled. The test results indicate that the power supply can work well under the different modes, the long-term stability of current rating reached 21 ppm, and the current ripple was less than 0.000 4, exceeding the design index.