To solve the problems of low similarity of historical trajectories and low prediction accuracy in vessel trajectory prediction, a trajectory prediction algorithm vSeq2Seq based on Sequence-to-Sequence (Seq2Seq) model is proposed.Firstly, the first-order differential method is used to process the AIS data, so as to reduce time dependence, weaken the impact of communication delays, and highlight the rules of vessel movement.Then, the sliding window method is used to process the data, a data set of the model is built, and the trajectory prediction with variable step sizes is conducted through Seq2Seq model.The experimental results show that the vSeq2Seq algorithm can extract the features from varied trajectories of the vessels, changing the prediction step size in different motion states of vessels to predict flexibly.Compared with that of the traditional LSTM and GRU models, the prediction accuracy is significantly improved.