Abstract: The heavy ion accelerator constrains particles by magnetic field, and the magnet power supply is the important part for making magnetic field. Therefore, the magnet power supply control system needs high efficiency, high stability and high accuracy. The magnet power supply response operated according to accelerator’s cycle. The magnet power supply control system for heavy ion accelerator was developed. The magnet power supply control timing of heavy ion accelerator is consistent with the control cycle of heavy ion accelerator control system. And the synchronous timing system triggers magnet power supply. All control data of magnet power supply (such as synchronous event data and waveform data) are obtained from center oracle database of heavy ion accelerator. Once the synchronous timing system triggers magnet power supply, the magnet power supply controller will read control data from RAM of ARM controller and process it by interpolation to control power supply. The precision of control system synchronization is 1 μs, and ripple is 100 ppm. It can meet requirement of heavy ion accelerator experiments.