Ultra-precision stage system is a critical component of a wafer scanner, including the wafer stage and the reticle stage. The synchronous performance of the wafer stage and reticle stage significantly affects the overlay and critical dimension uniformity of the machine. A moving-average-and-standard-deviation-based iterative learning control (MASD-ILC) method has been proposed. The method can reduce synchronous errors and suppress thrust ripple. The convergence principle and conditions of the method along the time axis and the iteration axis have been proved. The effects of the learning gain and weights have been discussed. The effectiveness of the proposed method has been verified through simulations. Compared with the e-ILC, MASD-ILC demonstrates faster convergence speed, smaller convergence error, and better robustness. MASD of the system based on MASD-ILC is reduced from 31.56nm to 0.10nm. Considering the thrust perturbation and model uncertainty, the convergence speed and convergence error of system based on MASD-ILC remain unaffected.