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This paper describes a controller design method for the inertially stabilized system of a tracking radar. Its aim is to track a reference target trajectory with high accuracy while isolating rigid body rotational motions of a host ship. First, we investigate the trajectory generation problem to make the control input for a target tracking on the moving base. Second, dynamic equations of motion are formulated by the spring-mass-damper system to include rigid body dynamics as well as structural flexibility. The unknown parameters of dynamic equations are estimated with experimental input and output data by minimizing a predicted error. Third, mixed sensitivity H∞ robust controllers are designed to meet the conflict requirements of robustness and performance in the face of uncertainty. Finally, the proposed optimal controllers demonstrate the effectiveness of design methodology, and show high performance by numerical and experimental results.