An automatic beam alignment system based on relative reference points is developed for the Thomson scattering system on Keda Torus eXperiment. Two critical apertures around the vacuum vessel are designed to shield stray light, and a probe beam is required to go through the centers of these two apertures, which are the reference points for alignment. Since these two apertures are coated with light absorbing materials, three fibers with glowing tips are employed to indicate the centers of two apertures. CMOS cameras are used to monitor beam deviations. The misalignment correction is achieved by driving piezomotor mirror mounts via a program developed with LabVIEW, which includes the image acquisition and processing module and the deviation correction module. As a result, this system can correct beam misalignment in less than 20 s and suppress the long-term drift of laser pointing in ±10 μrad. Also, this system has the capability to correct up to about 2.3 mm of camera shift with our experiment condition.