The Automatic Identification System (AIS) has become a key data source for ship behavior monitoring and maritime traffic management, widely used in trajectory prediction and anomaly detection. However, AIS data suffer from issues such as spatial sparsity, heterogeneous features, variable message formats, and irregular sampling intervals, while vessel trajectories are characterized by strong spatial–temporal dependencies. These factors pose significant challenges for efficient and accurate modeling. To address this issue, we propose a lightweight vessel trajectory prediction framework that integrates Spatial–Temporal Identity encoding with an MLP-Mixer architecture. The framework discretizes spatial and temporal features into structured IDs and uses dual MLP modules to model temporal dependencies and feature interactions without relying on convolution or attention mechanisms. Experiments on a large-scale real-world AIS dataset demonstrate that the proposed STID-Mixer achieves superior accuracy, training efficiency, and generalization capability compared to representative baseline models. The method offers a compact and deployable solution for large-scale maritime trajectory modeling.