To address the uncontrollable risks associated with the overreliance on ship operators’ driving in current ship safety braking methods, this study aims to reduce the impact of operator fatigue on navigation safety. Firstly, this study established a human–ship–environment monitoring system with functional and technical architecture, emphasizing the investigation of a ship braking model that integrates brain fatigue monitoring using electroencephalography (EEG) to reduce braking safety risks during navigation. Subsequently, the Stroop task experiment was employed to induce fatigue responses in drivers. By utilizing principal component analysis (PCA) to reduce dimensionality across multiple channels of the data acquisition device, this study extracted centroid frequency (CF) and power spectral entropy (PSE) features from channels 7 and 10. Additionally, a correlation analysis was conducted between these features and the Fatigue Severity Scale (FSS), a five-point scale for assessing fatigue severity in the subjects. This study established a model for scoring driver fatigue levels by selecting the three features with the highest correlation and utilizing ridge regression. The human–ship–environment monitoring system and fatigue prediction model proposed in this study, combined with the ship braking model, achieve a safer and more controllable ship braking process. By real-time monitoring and prediction of driver fatigue, appropriate measures can be taken in a timely manner to ensure navigation safety and driver health.