A novel marine transportation network based on high-dimensional AIS data with a multi-level clustering algorithm is proposed to discover important waypoints in trajectories based on selected navigation features. This network contains two parts: the calculation of major nodes with CLIQUE and BIRCH clustering methods and navigation network construction with edge construction theory. Unlike the state-of-art work for navigation clustering with only ship coordinate, the proposed method contains more high-dimensional features such as drafting, weather, and fuel consumption. By comparing the historical AIS data, more than 220,133 lines of data in 30 days were used to extract 440 major nodal points in less than 4 minutes with ordinary PC specs (i5 processer). The proposed method can be performed on more dimensional data for better ship path planning or even national economic analysis. Current work has shown good performance on complex ship trajectories distinction and great potential for future shipping transportation market analytical predictions.