The perception of risks is a prerequisite for establishing an intelligent ship navigation system based on ship-shore cooperation. According to the research conclusions on the ship-shore collaboration, the technical characteristics of the intelligent ship navigation system, and the analysis of the test results of the ship “ZHI FEI” featured with intelligent navigation, we study and construct the conceptual model and mathematical expression model for risk evolution of the intelligent ship navigation. We further explore the unmanned trend, the general law, and the characteristics of risk evolution based on navigation scenarios and chain effects. The present study provides insight into the risk perception, management, and government governance of intelligent ship navigation and the construction of an intelligent ship navigation system based on ship-shore collaboration.