Electro-Mechanical Actuators (EMA) have attracted growing attention with their increasing incorporation in More Electric Aircraft. The performance degradation assessment of EMA needs to be studied, in which EMA motor voltage is an essential parameter, to ensure its reliability and safety of EMA. However, deviation exists between motor voltage monitoring data and real motor voltage due to electromagnetic interference. To reduce the deviation, EMA motor voltage estimation generally requires an accurate voltage state equation which is difficult to obtain due to the complexity of EMA. To address this problem, a Feature-aided Kalman Filter (FAKF) method is proposed, in which the state equation is substituted by a physical model of current and voltage. Consequently, voltage state data can be obtained through current monitoring data and a current–voltage model. Furthermore, voltage estimation can be implemented by utilizing voltage state data and voltage monitoring data. To validate the effectiveness of the FAKF-based estimation method, experiments have been conducted based on the published data set from NASA’s Flyable Electro-Mechanical Actuator (FLEA) test stand. The experiment results demonstrate that the proposed method has good performance in EMA motor voltage estimation.