The navigational condition of the Nanjing Yangtze River Bridge is complicated with high safety risk. It is of great significance to master the navigation rules of ships for maritime surveillance and waterway design. Applying a parallel approach developed for calculating the density of ship trajectories in the Nanjing Yangtze River Bridge waters based on AIS big data，we recognize the distribution of the regular routes of ships of different sizes in different seasons，and find that most ships follow the navigation rules of the Nanjing Yangtze River Bridge waters in general. Compared to small ships，large ships are more formal in sailing across the bridge. When passing through the bridge span，the position of large ships is more centered，the angle between the large ships′ bow direction and the normal direction of the bridge axis is larger. Meanwhile，the overlap between the lane boundary of the large ships and the designed waterway is much higher than that of small ships. We also find that the ships prefer to take a northerly route in the flood season and a southerly route in the dry season. With the decrease of water level，ship tracks gradually change to the south.