In the current landscape, autonomous navigation systems face challenges due to incomplete functionality and low integration. They also lack a comprehensive, real-time, and accurate navigation risk assessment, while operating independently from one another. To address these issues, a multi-functional and practical adaptive collision avoidance decision-making system for autonomous ships is developed in this paper. The system primarily relies on the electronic navigational chart (ENC) to effectively display the ship’s navigation situation. It establishes a collision avoidance decision-making model centered around the own ship, offering collision risk analysis, avoidance methods, and optimal timing to ensure safe navigation. The system efficiently integrates and processes multimodal maritime data from various devices, utilizing ontology-based approaches for comprehensive navigation situation understanding, which integration provides invaluable support for intelligent decision-making processes. With a user-friendly interface, excellent portability, and cross-platform interoperability, this system has undergone collaborative efforts and joint debugging with China Shipbuilding Navigation Technology Co., Ltd. during the project’s first and second phases. Notably, the system has been successfully implemented on the “High-performance Integrated Bridge System” platform of China Shipbuilding Navigation, showcasing its potential for advancement from principle prototype development to actual equipment application. By offering accurate collision avoidance decision support, this system significantly contributes to enhancing the safety of ship navigation.