The invention discloses a system and a method for driving a micro-magnetic device by a multi-rotating permanent magnet, and relates to the field of intelligent control. In the invention, a permanent magnet is used as a field source, a driving circuit drives the permanent magnet to rotate so as to control a micro-magnetic device in any direction, and no input power exists, so that no heat is generated near the working space. Therefore, the application can be applied even in temperature sensitive applications. Compared with electromagnetic driving which depends on the size of the working space,the permanent magnet can generate about 10-20 times of field strength and 2-3 times of gradient force, has wide application range, and also is simple in structure, low in cost, free from translation part, high in precision and good in stability. Meanwhile, in combination of host computer control, the system can quickly find out the optimal control input required for generating the expected field strength and force, and can monitor the motion of the micro-magnetic device in real time by using a camera.