Abstract: Objectives Intelligent ship navigation serves as a foundational technology enabling the intelligent and green transformation of the maritime industry. This field currently grapples with two critical challenges: the disconnection between navigation and machinery systems, which impedes deep integration of energy efficiency with voyage control, and the ill-defined ship-shore coordination, which hinders scalable deployment. To address these issues, this paper conducts a systematic study on the architecture design of intelligent ship navigation systems. Methods First, it delineates the conceptual boundaries between “intelligent navigation” and “intelligent sailing” and introduces the “Navigation-Machinery Integration” philosophy as a core design paradigm, defining its essential characteristics and system scope. Subsequently, a novel intelligent navigation architecture under a ship-shore collaborative framework is proposed. This includes a three-tier onboard evolution path (“Enhanced - Assisted - Autonomous Navigation”) and a corresponding three-level shore-based control paradigm (“Monitoring - Remote Control - Navigation Control”). A functional adaptation matrix mapping asymmetric ship-shore relationships is established to clarify applicable scenarios for different operational modes. Furthermore, the paper analyzes key enabling technologies required for implementation, such as environmental perception and decision-making control. Results This research clarifies the core principles and architectural logic of intelligent ship navigation systems, defines functional adaptation for effective ship-shore synergy. Conclusions This research provides theoretical and technical foundations for engineering implementation and industry standard development. The findings contribute significantly to advancing next-generation intelligent shipping ecosystems.