<p>Electro-optical tracking systems have been widely used in the cutting-edge domains of free space environment detection and communication owing to their exceptional performance. However, external disturbances often significantly impact the working accuracy of these systems. As their scope of application continues to broaden, increasingly complex operating conditions introduce more intricate environments and disturbances. This paper introduces a composite control structure of an enhanced error-based observer, rooted in the repetitive control strategy, tailored for two types of complex disturbances: periodic harmonic disturbance and narrow-band peak periodic disturbance. This structure not only ensures the system’s stability, but also suppresses periodic disturbances across multiple frequencies, effectively addressing the challenge that current disturbance suppression methods face in mitigating complex periodic disturbances. Moreover, necessary proofs are provided and an experimental platform is established for the electro-optical system, demonstrating the efficacy and reliability of the proposed control methods under various conditions.</p>