The intraoperative movement of target organs is currently a key and difficult problem that restricts clinical surgery diagnosis and treatment, especially radiotherapy. Unexpected posture changes can cause the deviation of the target area during the operation, thereby affecting the treatment effect and even causing severe complications. Therefore, it is necessary to track the movement of target organs in real-time and accurately to improve the effect and safety of the surgical treatment. This paper proposes an intraoperative organ motion tracking method based on the fusion of inertial navigation and electromagnetic navigation., which can directly measure the target organ's movement under non-invasive or minimally invasive conditions using the human natural cavity. The proposed method for identifying the magnetic field's interference state uses the extended Kalman filter to fuse the inertial measurement unit and the electromagnetic positioning information to achieve target organ movement tracking under different interference conditions. It effectively improved the real-time and robustness of intraoperative organ tracking. Simultaneously, based on the 9-axis inertial measurement unit and a 6-DOF electromagnetic positioning system, the catheter-type target organ tracker was developed, and then under the simulated electromagnetic interference environment, dynamic and static verification experiments were carried out, respectively. The maximum tracking error of displacement and attitude is 2.75 mm and 0.127 rad, respectively, under severe electromagnetic disturbance through experiments. Under non-electromagnetic interference conditions, its displacement and attitude's maximum tracking errors are 0.94 mm and 0.011 rad, respectively. The results prove that the target organ tracking method based on the fusion of inertial navigation and electromagnetic navigation is feasible. It can realize the tracking and measurement of the target organ's movement within the clinical permission error range.INDEX TERMS Inertial navigation, target organ tracking, intraoperative navigation; fusion algorithm.