A kind of beam automatic alignment method used for double path amplification in an electron pumped excimer laser system was presented to ensure the beams from the amplifiers to transfer in a designed direction and irradiate on a target stably and accurately. As excimer laser amplifiers had no natural alignment references, an image-relaying structure with two cross-hairs was proposed, in which the cross-hair on the input beam was regarded as the near-field reference while the cross-hair of output beam was regarded as the far-field reference. Then, an alignment beam path was designed and the software was compiled. Furthermore, the automatic alignment experiment of double paths in electron pumped excimer laser amplifier was performed and the correlative influence factors and the alignment precision were analysed. Experimental results indicate that the automatic alignment system can achieve the beam transmission given in short time, the accuracy of alignment system is 0.63 μrad and the beam maximum restoration error is 13.75 μm. Obtained results satisfy the demand of beam alignment.