A modified Extended State Kalman Filter (ESKF)-based Model Predictive Control (MPC) algorithm is introduced to tailor the enhanced disturbance suppression in electro-optical tracking systems. Traditional control techniques, although robust, often struggle in scenarios with concurrent internal, external disturbances, and sensor noise. The proposed algorithm effectively overcomes these limitations by precisely estimating system states and actively mitigating disturbances, thus significantly boosting noise and perturbation control resilience. The primary contributions of this study include the integration of ESKF for accurate system state and disturbance estimation in noisy environments, the embedding of an ESKF estimation-compensation loop to simulate an improved disturbance-free system, and a simplified modeling approach for the controlled device. This designed structure minimizes the reliance on extensive system identification, easing the predictive control model-based constraints. Moreover, the approach incorporates total disturbance estimation into the optimization problem, safeguarding against actuator damage and ensuring high tracking accuracy. Through rigorous simulations and experiments, the ESKF-based MPC has demonstrated enhanced model error tolerance and superior disturbance suppression capabilities. Comparative analyses under varying model parameters and external disturbances highlight its exceptional trajectory tracking performance, even in the presence of model uncertainties and external noise.