Ship trajectory prediction plays a key role in the early warning and safety of maritime traffic. It is a necessary assistant tool that can forecast a ship’s trajectory in a certain period to prevent ship collision. However, highly precise prediction of long-term ship trajectories is still a challenge. This study proposes a ship trajectory prediction model called ShipTrack-TVAE, which is based on a Variational Autoencoder (SocialVAE) and Transformer architecture. It aims to address ship trajectory prediction tasks in complex waterways. To enable the model to avoid potential collision risks, this study designs a collision avoidance mechanism, which comprehensively incorporates safety constraints related to the distance between ships into the loss function. The experimental results show that on the Qiongzhou Strait ship AIS dataset, the Average Displacement Error (ADE) of ShipTrack-TVAE improved by 21.85% compared to the current state-of-the-art trajectory prediction model, SocialVAE, while the Final Displacement Error (FDE) improved by 17.83%. The experimental results demonstrate that the ShipTrack-TVAE model can effectively improve the prediction accuracy of short-term, medium-term, and long-term ship trajectories. It has excellent performance and provides a certain reference value for advancing unmanned ship collision avoidance.