With the increasing requirements for power supply function and performance from heavy ion accelerators, the hardware and software of the power supply digital controller based on FPGA have been upgrading for more than ten years, and it has been developed into the third-generation up to now. The first-generation controller adopted the centralized architecture. To realize the functions of high-precision power adjustment, fault detection and protection, external communication, etc., the system-on-a-programmable-chip based on NIOS II Dual CPU in a single FPGA was built. The second-generation controller adopted the multi-board high-speed interconnection architecture. The ARM-based system-on-a-programmable-chip was built in the FPGA of the regulation board. To facilitate the remote control of the power supply, the debugging interface and database based on the webpage were developed. The third-generation controller adopted the master-slave architecture based on high-speed optical fiber communication. It has realized the control of multi-module cascade power supply and high-speed data transmission, and its performance has been greatly improved.