To address the problem that the traditional angle tracking loop based on rate gyros has difficulties in tracking modern high-speed and large maneuvering targets, a novel control method of angle tracking system based on pre-filter was proposed by introducing the concept of Kalman filter. Firstly, the mathematical model was established in body LOS coordinates, and tracking state equations of the angle tracking system were derived. The target maneuver was described by the “current” statistical model, and the misalignment angle was selected as the only observed quantity according to the actual measurable conditions of the seeker. Then the internal factors of low accuracy and early divergence of the traditional angle tracking control method were analyzed, and the improved method of pre-filter was proposed. The discrete state estimator of Kalman filter was designed, and the online real-time iterative solution of seeker was realized. Finally, considering the scenarios that the target adopts different evasive maneuvering strategies accordingly under the attacks of the missile from three different angles, the tracking results were compared. Results show that the improved pre-filter control method could reduce the shock caused by target maneuvering, delay the divergence time of the angle tracking system, further increase the terminal control distance of the seeker, enhance the capability of the seeker against large maneuvering targets, and thus effectively improve the hit probability of the missile.