Ship trajectory prediction is a complex time series forecasting problem that necessitates models capable of accurately capturing both long-term trends and short-term fluctuations in vessel movements. While existing deep learning models excel in short-term predictions, they struggle with long-sequence time series forecasting (LSTF) due to difficulties in capturing long-term dependencies, resulting in significant prediction errors. This paper proposes the Informer-TP method, leveraging Automatic Identification System (AIS) data and based on the Informer model, to enhance the ability to capture long-term dependencies, thereby improving the accuracy of long-term ship trajectory predictions. Firstly, AIS data are preprocessed and divided into trajectory segments. Secondly, the time series is separated from the trajectory data in each segment and input into the model. The Informer model is utilized to improve long-term ship trajectory prediction ability, and the output mechanism is adjusted to enable predictions for each segment. Finally, the proposed model’s effectiveness is validated through comparisons with baseline models, and the influence of various sequence lengths $L_{token}$ on the Informer-TP model is explored. Experimental results show that compared with other models, the proposed model exhibits the lowest Mean Squared Error, Mean Absolute Error, and Haversine distance in long-term forecasting, demonstrating that the model can effectively capture long-term dependencies in the trajectories, thereby improving the accuracy of long-term vessel trajectory predictions. This provides an effective and feasible method for ensuring ship navigation safety and advancing intelligent shipping.