The exhaust gas recirculation (EGR) valve plays an important role in improving engine fuel economy and reducing emissions. In order to improve the positioning accuracy and robustness of the EGR valve under uncertain dynamics and external disturbances, this paper proposes a positioning servo system design for an electromotive (EM) EGR valve based on the Kalman filter. Taking a novel valve driven by a central winding limited angle torque motor (LATM) as the object, we have fully considered the influence of the motor rotor position and load current, as well as the magnetic field saturation and cogging effect, improved the existing LTAM model, and derived accurate torque expression. The parameter uncertainty of the above internal model and the external stochastic disturbance were unified as “total disturbance”, and a Kalman filter-based observer was designed for disturbance estimations and real-time feed-forward compensation. Furthermore, using non-contact magnetic angle measurements to obtain accurate valve position information, a position control model with real-time response and high accuracy was established. Numerous simulated and experimental data show that in the presence of ± 25% plant model parameter fluctuations and random shock-type disturbances, the servo system scheme proposed in this paper achieves a maximum position deviation of 0.3 mm, a repeatability of positioning accuracy after disturbances of 0.01 mm, and a disturbance recovery time of not more than 250 ms. In addition, the above performance is insensitive to the duration of the disturbance, which demonstrates the strong robustness, high accuracy, and excellent dynamic response capability of the proposed design.