This study aims to discuss a risk assessment of navigation safety for ferries. In this research, the risk factors (RFs) for the navigation safety of ferries are first investigated from relevant literature and ferry operational features. A fuzzy AHP (Analytic Hierarchical Process) approach is then proposed to weight those RFs, after which a continuous risk-matrix model is then developed to determine the RFs’ risk levels. Finally, to validate the practical application of the proposed model, ferries traveling across the Taiwan Strait were empirically investigated. The results may provide practical information for ferry operators to improve their safety performances. Further, the proposed risk assessment approach may provide references for related research in the safety management of short-distance passenger ships.