To obtain a good interference fringe contrast and high fidelity, an automated beam iterative alignment is achieved in scanning beam interference lithography (SBIL). To solve the problem of alignment failure caused by a large beam angle (or position) overshoot exceeding the detector range while also speeding up the convergence, a weighted iterative algorithm using a weight parameter that is changed linearly piecewise is proposed. The changes in the beam angle and position deviation during the alignment process based on different iterative algorithms are compared by experiment and simulation. The results show that the proposed iterative algorithm can be used to suppress the beam angle (or position) overshoot, avoiding alignment failure caused by over-ranging. In addition, the convergence speed can be effectively increased. The algorithm proposed can optimize the beam alignment process in SBIL.