Currently, intelligent ships are still in the early stages of development in terms of autonomous navigation and autonomous berthing, so almost no source of fault data can be obtained. Conducting an in-depth analysis of the failure modes of intelligent ships is critical to optimizing the design of smart ships and ensuring their normal and safe navigation. In this paper, the fixed-weight Failure Mode Effects and Criticality Analysis (FMECA) is combined with the decision-making trial and evaluation laboratory (DEMATEL) method to analyze the failure modes and effects of intelligent ship positioning systems. This combined method not only overcomes the failure of traditional FMECA methods to differentiate between severity, incidence, and detection rates but also allows the correlation of failure causes to be analyzed, bringing the results of the analysis closer to reality. Through the expert scoring of failure modes, the failure modes of this system are risk-ranked, and the key failure causes of this system are identified. Correlations between the critical failure causes are then considered. According to the analysis results, the high-accuracy attitude sensor was identified as the subsystem with the highest level of risk. Unavoidable, unknown failures and environmental factors were found to be key factors in causing positioning system failures. The conclusions can provide a reference for the design of equipment safety for intelligent ship positioning systems.