Electron cyclotron resonance heating (ECRH) system is one of the most important Tokamak auxiliary heating methods. However, there are growing demands for ECRH system as the physical experiments progress which meanwhile adds the difficulty of designing and building the control system of its power source. In this paper, the method of designing a control system based on Single Chip Microcomputer (SCM) and Field Programmable Gate Array (FPGA) is introduced according to its main requirements. The experimental results show that the control system in this paper achieves the conversion of different working modes, gets exact timing, and realizes the failure protection in 10us thus can be used in the ECRH system.