Magnetic field has been considered as a safe and promising method for remote control of medical robots in body. Systems that implement electromagnetic coils can provide wide control bandwidth and on-off capability. However, scaling-up the working space of such systems for clinical use and increasing energy efficiency to reduce heat generation have always been a challenging task. The design, modeling and control methods for a magnetic actuation system with multiple mobile electromagnetic coils with decoupled movements are introduced. The high flexibility of such configuration and the proposed real-time control strategy enables the system to enlarge the working space by tracking the locomotion of the robot, deal with the irregularly shaped obstructions inside the working area, work with medical imaging systems for localization of the medical robots, generate various kind of magnetic field for actuation and conduct real-time optimization on coils' positions to enhance energy efficiency.