The electron beam welder is the application example of high-energy beam on the Welding equipment. In order to achieve a variety of logic control device, the traditional control system of the electron beam welder is based on PLC. It exist a lot of the disadvantages in the traditional control system of the electron beam welder. Especially, its welding energy has the simplex form of supply and the asynchronous with trajectory. In order to deal with this problem, it is developed the CNC system with the form of industrial personal computer (IPC) + motion control card in this paper. This CNC system can achieve the unified programming and synchronous control of the trajectory and two-energy magnitude: the focusing current and electron beam current. This CNC system can make up for the deficiency of the traditional control system and improve the efficiency and precision of weld. Feedback from its application on the electron beam welder indicates that it works reliably and the performance is satisfactory.