To improve the spatial resolution of X-ray real-time imaging systems, the optical micro-scanning technology is introduced into the existing imaging system and the optical micro-scanning X-ray real-time imaging system is built. The working principle of optical micro-scanning X-ray real-time imaging systems is introduced. The sub-pixel precision image registration technique is one of the key technology of successful application of the optical micro-scanning system. The principles, processes and concrete steps of frequency-domain windowing image registration method are introduced. Simulations with different registration algorithms for X-ray image are studied. Simulation results indicate indicate that the effectiveness of the image registration algorithm for X-ray image. The technique improves the accuracy of the actual X-ray image registration to a sub-pixel level and has a strong practical value.