Magnetic levitation can reduce particulate contamination that occurs during wafer transportation in the semiconductor manufacturing process. This technology radically eliminates contact between the wafer and the transport system, reducing friction, wear, and particle generation. Therefore, it is suitable for achieving high cleanliness in the ultra-fine line-width semiconductor production process and solving the need for particle removal in a vacuum environment. In this study, the roller and linear motion guide components of the wafer transfer system were replaced with a magnetic levitation module, and a robot arm was installed on top to transport a single wafer. A posture controller and a current controller were designed, and test equipment simulating the wafer transfer system was also manufactured and tested. Regarding mover and system identification, a sine sweep test was performed on the motion axis of the five degrees of freedom. Through the obtained system identification, it was possible to design the posture controller more precisely. Moreover, through levitation in standstill experiments and high-speed operation experiments, the wafer transport system can be used to verify dust-free high-speed transport and accurate positioning performance.