With the rapid development of the global economy and trade, the number of ships serving ports in China is increasing continuously. Port traffic is becoming busier, and ship behavior is more complex and changeable. The analysis of ship behavior patterns in port waters has become an urgent problem to improve the efficiency and safety of port areas. In this paper, through the full integration of ship trajectory and port geographic information, the behavior chain of a single ship across the whole process of entering and exiting the port is identified. The traffic complexities and dynamics can be further analyzed by grouping the movement patterns of large ships. Based on graph theory, the port areas can be described as a transportation network in which functional areas are nodes and fairways between different areas are edges. The traffic can be analyzed through the network structure characteristics, such as node degree, node weight, and edge weight, and by their similarities and differences. This methodology provides a quantitative analysis for exploring the behavior patterns of large ships as well as the various traffic complexities. A case study in Tianjin Port has been conducted to verify the proposed model. The results show that it can accurately analyze a ship behavior’s regularity, occasion, and correlation. It provides a theoretical reference for the port to schedule and formulate emergency plans.