The perception and acquisition of navigation-related information are essential for the safety of intelligent ship. To address the effectiveness of navigational information monitoring system designed for the intelligent ship, in the present study, a comprehensive evaluation methodology is proposed. The various functions designed for obtaining corresponding navigational information are reorganized to develop the structure of intelligent ship navigational information monitoring system, which is subjected to evaluate the effectiveness by analyzing the information behavior processes in this proposed system and the available information monitoring technologies applied on intelligent ships. The orthogonal exploratory analysis technique was applied to establish the functional relationship between system effectiveness and contributing subsystems, as a result, the contribution degree distribution of contributing subsystems identified for system effectiveness is obtained. Finally, an application of the proposed methodology verifies its feasibility in calculating system effectiveness and its potential to extend to intelligent ships at different levels. The present study provides a new perspective to understand the safety of intelligent ships, and the comprehensive evaluation methodology provides a new path for the effectiveness analysis of intelligent ship navigational information monitoring system.