For the improvement in the safety construction of the shipping system，it is necessary to build a seaworthiness analysis model for waterways and apply it to ships during navigation to evaluate the rationality of route planning and provide automatic and intelligent guidance for safe navigation of ships. Since the previous two-dimensional （2D）data cannot meet the needs of spatial analysis，we can obtain the navigable area of ships by performing spatial operations on the 3D track zone，3D underwater terrain，and 3D waterway element model that are constructed by AIS track line data and ship model parameters. On this basis，the collision risk index （CRI）for ships is introduced as the basis of early warning and decision analysis，and the seaworthiness analysis model is built. Taking the three-dimensional waterway of the Beijing-Hangzhou Canal （the Grand Canal）as the research object，we conduct the simulation experiment to verify the reliability and stability of the model.