As a new type of guidance technology, the strapdown imaging guidance technology, which helps improve the system reliability and reduce costs efficiently, has been paid great attention and developed quickly. However, the detecting information of strapdown seeker can’t be used to proportional navigation directly because it is coupled with missile attitude. A method to estimate the inertial Line-of-Sight (LOS) rate of strapdown imaging seeker based on Cubature Kalman filter (CKF) and Tracking-Differentiator (TD) was presented. As there were high nonlinearity in both state and measurement equations and more serious non-Gaussian noise in the measurements, the Extended Kalman filter (EKF) could not completely meet the requirements of filtering. Compared with EKF and Unscented Particle filter (UKF), CKF was a congruent method for states estimating in the conditions of nonlinearity and non-Gaussian noise. CKF was applied to estimate the LOS rate of strapdown imaging seeker. Because measurement noise of missile attitude will be reflected in estimation result, TD was used to decrease noise of the missile attitude measurements for improving the estimation precision. Monte Carlo simulation results show that the proposed method can improve the precision of guidance.