Real-time tracking for surgical instruments is required in modern inversion endoscope surgery. Compared with traditional tracking methods, the surgical navigation method based on inertial sensing can effectively avoid the limited tracking region caused by optical tracking (OPT), and overcome high sensitivity to magnetic disturbance in electromagnetic tracking (EMT). Meanwhile, the effect from the sensors’interference in both of orientation estimate and position determination is considered and the anti-interference technique achieving more stable output is improved. The experimental results show that even under magnetic disturbance, the orientation error is less than 3° and position error is less than 4 mm. Both of them meet the requirements of clinical applications.