The present invention relates to a magnetic drive system compatible with a C-arm, and more particularly, to a magnetic drive system compatible with a C-arm, and more particularly, to a magnetic drive system compatible with a C-arm, which uses a magnetic field to control a magnetic microrobot or a magnetic drive type catheter or guide wire. The magnetic drive system is applied to a C-arm, which is a mobile X-ray fluoroscopic imaging device, so that a microrobot in a human body using the C-arm can be controlled or a catheter operation can be performed.