In the manufacturing process of electron beam freeform fabrication, the temperature distribution of the part can be improved by scanning the forming area of the part with electron beam and controlling the heat input, and the annealing along the part can be realized to reduce the stress and control the deformation. The high-speed scanning system of electron beam is built by using industrial computer, waveform generator, scanning coil and its driving circuit, and dynamic focusing coil and its driving circuit. The functions of high-speed scanning and dynamic focusing of electron beam are realized. Based on LabVIEW, the control system of real time annealing scanning is developed, and the control method based on pixel lattice positioning and dynamic aggregation is proposed to realize the precise positioning and heat input control of electron beam scanning; The influence of different scanning paths on the temperature uniformity of the heat source is studied, and the temperature of the scanning area is measured by using multi-point synchronous temperature measurement circuit. The experimental results show that the scanning position and heat input can be accurately controlled by the electron beam real time annealing system, and the uniformity of the temperature distribution of the surface heat source can be significantly improved by optimizing the scanning path.