Wafer alignment is a critical process in ensuring precise positioning of wafers during manufacturing. However, its positioning accuracy is often compromised by residual vibrations caused by sudden changes in acceleration during the high-speed start and stop phases of the chuck. To address this challenge, this study first analyzes the contact characteristics of the chuck surface, develops a mathematical dynamic model for the wafer alignment chuck, and simulates the contact interactions and deformation between the wafer and chuck during motion. Based on this analysis, the relationship between the system’ s vacuum level, maximum rotational speed, and maximum rotational acceleration is explored to determine the wafer’ s amplitude and mode under various acceleration conditions. An acceleration constraint equation is derived, and a symmetric velocity curve for the wafer alignment is constructed using a third-order Bezier curve. Additionally, accounting for motor characteristic variations during acceleration and deceleration phases, the parameters of the symmetric velocity curve are optimized using a Pareto multi-objective genetic algorithm to create an asymmetric velocity curve. This approach helps to further suppress residual vibrations of the chuck, thereby enhancing positioning accuracy and operational efficiency. Simulation experiments confirm the improvement in operational efficiency with the proposed asymmetric velocity curve. A physical wafer alignment device is also built, and physical experiments demonstrate enhanced positioning accuracy and operational efficiency compared to traditional velocity curves. The experimental results show that the asymmetric velocity curve, which accounts for the dynamic characteristics of the chuck, effectively reduces residual vibrations, improving alignment accuracy to 0. 008 mm and reducing operation time by 0. . 14 s. These findings validate the effectiveness of the proposed method in improving wafer alignment performance.