Electromechanical actuators (EMAs), as the new generation of actuators, have an important impact on the safety of aircraft. With the development of measurement technology, a large amount of data provides a broad prospect for the data-based fault diagnosis method. However, the existence of redundant data increases the burden of software and hardware. Therefore, a semi-supervised sparse auto-encoder (SSAE) is employed to prune observed data based on sparsity analysis. Moreover, temporal and spatial relationships are explored by a multi-channel long short-term network to build a time series model, so as to perform fault detection and isolation based on the difference between its estimated and observed values. Due to its sparse feature extraction capability, the SSAE can improve the fault isolation accuracy while pruning observed data. Verification results confirm that the proposed method can effectively diagnose EMA faults.