In this article, an electromagnetic actuator is proposed to improve the driving performance of magnetic levitation transportation applied to ultra-clean manufacturing. The electromagnetic actuator mainly includes the stator with the Halbach array and the mover with a symmetrical structure. First, the actuator principle and structure are illustrated. Afterward, in order to select a suitable secondary structure and analyze the characteristics of the actuator, the electromagnetic characteristics of actuators with different secondary structures are analyzed by the finite element method (FEM). Analysis results show that the actuator adopting the secondary structure with a Halbach array will increase the electromagnetic force and working stability. The secondary with the three-section Halbach array is selected for the electromagnetic actuator. Then, the influence of secondary permanent magnet (PM) thickness on the electromagnetic force is analyzed by FEM. The results indicate that the increase in PM thickness will lead to increased electromagnetic force and decreased utilization ratio of PM. Finally, a prototype of an electromagnetic actuator is built, and experiments are implemented. The correctness of the theoretical analysis and the effectiveness of the electromagnetic actuator are verified by experimental results.