A capsule endoscope magnetic control system includes a control handle assembly, and a capsule endoscope having a controlled unit, a wireless power receiving unit, an image capturing unit, a processing unit, and a wireless communication unit. The control handle assembly includes a magnetic control unit for generating a magnetic field and a wireless power transmission unit for generating electromagnetic waves. After the capsule endoscope is placed inside a test object, the controlled unit fixed to the outside of the capsule endoscope changes the rotational direction of the capsule endoscope according to the changes in the magnetic field. The wireless power receiving unit generates an induced current. The image capturing unit generates an image data, which is received and converted by the processing unit into an image signal, which is transmitted by the wireless communication unit to the control handle assembly. Therefore, the capsule endoscope has a long battery life.