In inversion endoscope surgery, high-accuracy tracking for medical instruments is demanded. Traditional electromagnetic tracking (EMT) methods are confined by their low robustness and high complexity, which restrict EMT from clinical application. To solve the problems, an inertial measurement unit (IMU) is added to EMT system to realize multi-sensing tracking. The effective fusion techniques provide anti-interference ability for the tracking system. At the same time, IMU can also help to simplify EMT and improve practicality on system level. The experimental results show that orientation error is less than 1°, and position error is less than 3 mm. Even under disturbances, orientation error can be controlled under 3.5°, which meets the clinical requirements.