A system for controlling a position of a micro-robot using a dual source X-ray image device is provided. The system includes a main body having dual X-ray sources, an image pick-up unit using X-rays from the dual sources, a coil unit provided in the main body so as to generate a drive signal to drive the micro-robot, a drive unit for driving the image pick-up unit and the coil unit relative to the main unit, and a control unit controlling the coil unit or the drive unit based on image data obtained from the image pick-up unit to control a position of the micro-robot.