Abstract: The fifth-generation stationary electron beam computed tomography (EBCT) can obtain CT imaging in the static state of the detected object, X-ray source and detector. This EBCT imaging method can be applied to the CT detection of deformable objects such as powder materials and living biological samples, as well as the rapid CT detection of logistics packages and pipelines in service. High-precision electron beam deflection system is one of the key technologies for miniaturizing low-cost multi-focus X-ray source for a stationary CT system. Based on Maxwell’s theory of electromagnetic field interaction, the defocusing, distortion and sensitivity characteristics of electron beam in small deflection angle, paraxial region and mean magnetic field were studied theoretically. The physical parameters affecting the repetition accuracy of focal position of electron beam scanning system and the scanning deflection of electron beam on target plane were discussed, and the linear relationship between the transfer distance and the deflection coil current was also studied. A small high-precision electron beam deflection scanning system for multi-focus X-ray source system was designed and fabricated. The DR projection image sequences of a 0.1 mm diameter standard needle gauge were acquired by electron beam scanning method. Our experimental results show that the electron beam deflection system has good deflection linearity and the transfer distance is proportional to magnetic field intensity of origin, rather than the initial condition of the electron beam. The beam deflection system controls the electron beam deflection scanning, and 250 X-ray projections of a fused fuse (Ø100 μm) were obtained. The fifth-generation stationary three dimensional CT images were reconstructed.