Abstract: This paper proposes an optical-inertial hybrid tracking method to solve the occlusion problem in optical tracking, in which the optical tracking is used to compensate the bias in inertial sensors when there is no occlusion and an FIR filter is used to compensate for the noises of the inertial sensors. The orientation of the target is calculated in a Kalman filter, the position of visible marker points and orientation from inertial tracking unit are fused for calculating the 6 degree-of-freedom motion of targets. Experimental result shows that the proposed system can track the targets with or without occlusion and display the surgical navigation image coordinated to the targets to the users.