The wafer stage in dual-stage lithographic system is an air-bearing servo motion platform requiring high positioning accuracy and high transient performance. However, the residual vibration, resulting from almost zero damping, high velocity, parallel decoupling structure, and direct drive, brings about unacceptable overshoot and settling time. To suppress these unfavorable elements in high dynamic motion, a novel motion profile planning method combined with input shaping is proposed in this paper. Firstly, a trajectory named all free S-curve (AFS-curve) is derived, which has less constraints and better performance than traditional S-curve profile. Then, AFS-curve combined with a zero vibration shaper (ZV) is developed to further suppress residual vibration. Due to the very complex parameter adjustment, the online tuning may cause system oscillation that leads to damage of the precision stage. This paper, furthermore, proposes an online-offline method to optimize the parameters in the motion profile. Online step is performed to collect input and output data. Offline step includes the system model identification based on I/O data and parameter self-learning based on particle swarm optimization (PSO). The simulation and experimental results indicate that the proposed method achieves significant reduction of the positioning time and the overshoot in the dual-stage system.