To reduce the exchange time of dual-stage lithography, a modified fifth-order S-curve planning method and a minimum-time and minimum-jerk control method are proposed. The dual-driver and dual-bridge exchange method of the wafer stages is analyzed, and the wafer stages on the exposure position and pre-alignment position make five point-to-point movements to complete the exchange process. A minimum-jerk optimization index is added to fifth-order S-curve based on numerical integration method, and a modified fifth-order S-curve planning algorithm is proposed to ensure the acceleration curve is smooth. Aiming at a minimum-time and minimum-jerk criterion, an optimal control system is designed to reduce the exchange time and overcome the default of controlling the acceleration mutation only by the minimum-time Bang-Bang control. Simulation and experiment results show that the exchange process can be realized by trajectory planning and optimal control method. The acceleration curve of modified fifth-order S-curve is the most smooth, and minimum-time and minimum-jerk optimal control system can achieve a shorter exchange time.