To meet the practical demands of autonomous ships for self-identifying navigation scenarios at sea, an adaptive recognition method for navigation scenarios in port waters based on electronic nautical charts is proposed. Firstly, by systematically analyzing the navigation characteristics of port waters, the ship navigation process is divided into eight scenarios: entering the port, leaving the port, navigating in the channel, entering and leaving the anchorage, anchoring, berthing, unberthing and mooring in the port. Secondly, a scene determination rule is established based on the characteristics of objects and their relative positions, and an adaptive recognition model integrating geometric relationships and dynamic parameters is constructed. Finally, the proposed method is verified based on the AIS historical trajectory data of 100 ships entering and leaving the waters of Yantai Port. The results show that the precision rate of this method for port navigation scenarios reaches 95.6%, and the delay is reduced to 12 ms. It can provide real-time necessary navigation scenario information and high-precision navigation environment perception support for the autonomous navigation system of ships sailing in the port area.