Beam alignment is one of the key techniques in the scanning beam interference lithography system. The coincidence degree between the position and the angle of two exposure beams directly affects the groove quality of the produced grating mask. In view of the mutual coupling between the two dimensions of motion in beam adjustment, the convergence condition of the alignment algorithm is derived, and the influence of assembly error between the reflector and the decoupling plane on the alignment performance is analyzed. The analysis shows that due to the presence of assembly error, the performance of the beam alignment system declines, and even leads to the divergence of the alignment algorithm. The convergence of the system can be optimized by adjusting the ratio L₂/L₁, where L₁ is the distance between mirror M₁ and decoupling plane, and L₂ is the distance between mirror M₂ and decoupling plane. The experimental results show that when L₂/L₁ is large, performance of the alignment system is poor and the convergence is slow. When L₂/L₁ is relatively small, the beam alignment system can quickly converge to the target position, and the alignment of the beam is effective. The deduction and simulation analysis can provide theoretical guidance for the design of beam alignment systems and whole exposure light paths.