Disturbance rejection rate(DRR) not only affects output accuracy of the seeker but also worsens the performance of missile guidance system. The main factor which causes the problem of DRR with laser gimbaled seeker is the disturbing torque. Aiming at the problem caused by DRR, a real time method for compensating disturbing torque based on Strong Tracking Unscented Kalman Filter(STUKF) was proposed. With the analysis of gimbaled seeker′s operational principle and disturbing torque′s mechanism, the nonlinear filter model for estimating the damping and spring torque was built. The STUKF algorithm was adopted to estimate the disturbing torque quickly and accurately, and the DRR was inhibited by the proposed method. Finally a math simulation and a hardware-in-loop simulation were put forward, the simulation results indicate that the accuracy of the seeker′s output and stable performance of guidance system are improved after the disturbing torque is compensated.