In order to improve alignment accuracy of exposure beams in the scanning beam interference lithography system and guarantee quality of the fabricated grating mask groove shape, an alignment error model of exposure beams is established and used to analyze the beam alignment error. Meanwhile, to meet the requirement of the system for beam overlapping accuracy, an automatic beam alignment system is designed and fabricated, and alignment experiments are conducted on the exposure beams. Analysis results show that the exposure contrast on the grating substrate surface decreases obviously when the beams have large alignment errors. Under the exposure mode of stepping-scanning, uneven exposure appears at different positions of the photoresist surface, which influencing the quality of grating mask groove shape. The designed alignment system can adjust the beam angles and positions. The system shows good convergence performance as a whole. After multi-step adjustment, the position alignment accuracy of the beams exceeds 10 μm, and the angle alignment accuracy of the beams exceeds 9 μrad. The alignment accuracy of exposure beams satisfies system requirements and the expected purpose is achieved.