When conducting accident analysis, the assessment of risk is one of the important links. Moreover, with regards to crew training, risk cognition is also an important training subject. However, most of the existing researches only rely on a single or a few data sources. It is necessary to fuse the collected multi-source data to obtain a more comprehensive risk evaluation model. There are few studies on the three-dimensional (3D) multi-modal data-fusion-based trajectory risk cognition. In this paper, a fuzzy logic-based trajectory risk cognition method is proposed based on multi-model spatial data fusion and accident data mining. First, the necessity of multi-model spatial data fusion is analysed and a data-fusion-based scene map is constructed. Second, a risk cognition model fused by multiple factors, multi-dimensional spatial calculations as well as data mining results is proposed, including a novel ship boundary calculation approach and newly constructed factors. Finally, a radar chart is used to illustrate the risk, and a risk cognition system is developed. Experiment results confirm the effectiveness of the method. It can be applied to train human operators of unmanned ship systems.