Disclosed is a method for tracking an affected area and a surgical instrument in which locations of the affected area and the surgical instrument are macro-traced by tracking sensors and markers, and using a stereo microscope with the macro-traced images of the affected area and the surgical instrument, allowing the locations thereof to be more accurately and precisely micro-traced. The method for tracking an affected area and a surgical instrument comprises: a macro-tracking step for detecting, via tracking sensors, energy generated from a plurality of markers attached to the affected area and the surgical instrument, and tracing the locations thereof by means of a processor; an image input step for filming images of the affected area and the surgical instrument traced via tracking sensors in the macro-tracking step, and inputting images of the affected area and the surgical instrument filmed via the tracking sensors into the stereo display unit of a microscope by means of the processor; and a micro-tracking step for tracing, with the coordinate system of the microscope as a reference, the locations of the affected area and the surgical instrument by means of the images entered into the stereo display unit of the microscope.