The safety of maritime transportation has become increasingly important in recent decades. In this paper, a decision model (a multi-objective and multi-layer fuzzy optimisation model) for navigation risk in different sea areas is established. This is done according to the evaluation index system based on relative data extracted and analysed from Automatic Identification Systems (AIS) information and the multi-objective and multi-layer fuzzy optimisation theory. Then, sorted by an optimal relative membership degree vector and calculated from lower layer to higher layer, the sea areas which have higher navigation risk are selected. Finally, the decision model is shown to be scientific and practical since the results from it are basically consistent with real traffic in Chengshantou waters and the results from the fuzzy comprehensive evaluation model. With the decision model, navigation risk judgments in different sea areas can be offered. It can also provide decision making references to the design of ship routing systems, the layout of search and rescue sites, the configuration of rescue forces and the administration of navigation safety.