The conventional scroll compressor cannot run oil-free because of wear and tear and lubrication problems during operation due to some parts, such as anti-rotation devices. The magnetic drive oil-free scroll compressor (MDOFSC) uses a contactless drive method to avoid this drawback. In order to solve the swing problem of the orbiting scroll during the operation of the MDOFSC, decentralized control and centralized control are used to study the trajectory tracking characteristics. Firstly, the structure and working principle of the MDOFSC are introduced, and the system’s magnetic circuit and differential control principle are analyzed. Then, the dynamic model of the MDOFSC under the condition of non-compressed gas is established, and the coordinate matrix decoupling method is used to analyze the relationship between the degree of freedom of the system and the measurement distance of the displacement sensor. Finally, the system is simulated and experimentally studied under centralized PID control, and the experimental comparison study between decentralized control and centralized control is conducted. The results show that centralized control dramatically improves the trajectory control ability of the system.