Abstract: Electron Cyclotron Resonance Heating (ECRH) system is one of the most important Tokamak auxiliary heating methods. However, with the development of physical experiments progress, there are growing stringent requirements for ECRH system and high-voltage power supply system, at the same time, more difficulty of the control and protection of high-voltage power supply. In this paper, according to the requirements of -60 kV/50 A PSM high-voltage power supply, a control system based on MCU and FPGA is developed, which not only satisfies all working modes of the power supply system, especially the requirements of 1 kHz modulation, but also meets the requirements of logic control and fast protection for gyrotron test bench. The experimental results show good logic structure and reliable operation of the power supply and control system and it can fit the requirements of logic control, timing and fast protection for gyrotron test bench.