Generator control system decides whether the generator can work as usual or not, as well as its stability of performance. Both types of generators control system composed of the transistor and DSP are sensitive to outward electromagnetic interference, directly related to the generator performance. In this text, we first analyze the electromagnetic interference threat generator control system of transistor type may face, then design a electromagnetic protection plan for the intake, the panel and the sense organ. This work is of great significance in improving its electromagnetic protection ability and stability of performance.