The semantic expression of ship behaviors is the basis to realize the intelligent recognition and knowledge reasoning of the water traffic situation. In order to achieve the semantic expression and abstraction of the spatial-temporal motion features of ships and improve the semantic conversion method of ship trajectories, a cognitive computing model of ship behavior semantics was proposed. By integrating the spatial-temporal data of ship trajectory and navigation environment information, based on the ship trajectory unit, the spatial-temporal behavior of the ship was abstracted to atomic behavior, topological behavior, and traffic behavior according to the theory of space topology, considering the motion states, spatial topological characteristics, and behavioral semantic characteristics. The conceptual modeling, semantic description, and formalization expression were carried out at different levels from spatial-temporal trajectory to semantic behavior of the ship. Finally, different types of navigation behaviors of ships in port waters were verified based on the semantic model. Results show that the model could be used to model and express ship behaviors with different motion features and spatial topological features in port waters, and five typical traffic behaviors were extracted, which indicates that the model is reasonable and applicable to the cognitive modeling of ship behaviors. The model can provide theoretical and methodological basis for semantic recognition and knowledge calculation of ship behaviors to realize the semantic calculation and cognitive reasoning of advanced ship behaviors.