The quality of Automatic Identification System (AIS) data is of fundamental importance for maritime situational awareness and navigation risk assessment. To improve operational efficiency, a deep learning method based on Bi-directional Long Short-Term Memory Recurrent Neural Networks (BLSTM-RNNs) is proposed and applied in AIS trajectory data restoration. Case studies have been conducted in two distinct reaches of the Yangtze River and the capability of the proposed method has been evaluated. Comparisons have been made between the BLSTM-RNNs-based method and the linear method and classic Artificial Neural Networks. Satisfactory results have been obtained by all methods in straight waterways while the BLSTM-RNNs-based method is superior in meandering waterways. Owing to the bi-directional prediction nature of the proposed method, ship trajectory restoration is favourable for complicated geometry and multiple missing points cases. The residual error of the proposed model is computed through Euclidean distance which decreases to an order of 10 m. It is considered that the present study could provide an alternative method for improving AIS data quality, thus ensuring its completeness and reliability.