A laser beam automatic alignment system is applied in a multipass amplifier of the SG-III prototype laser. Considering the requirements of the SG-III prototype facility, by combining the general techniques of the laser beam automatic alignment system, according to the image relayed of the pinholes in the spatial filter, and utilizing the optical position and the spatial distribution of the four pinholes of the main spatial filter in the multipass amplifier of the SG-III prototype, a reasonable and optimized scheme for automatic aligning multipass beam paths is presented. It is demonstrated on the multipass amplifier experimental system. ?2004 Society of Photo-Optical Instrumentation Engineers.