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In order to reduce the influence of subjective factors on navigation risk assessment, we present a novel scheme based on the fuzzy Dempster–Shafer evidence theory in this article. At first, we deduce the fuzzy set after analyzing various indicators in actual vessel navigation as an example. What’s more, the current data can be adaptively transformed into quantitative information on the basis of two-order membership functions. Considering the inherent defects of standard Dempster–Shafer evidence framework, the assessment process is improved to combine the uncertain and conflicting evidences from available indicators to make reliable decision. Further, three propositions are derived to explain the proposed scheme step by step. Finally, the numerical study results indicate that the proposed scheme has satisfactory performance for vessel navigation risk assessment in the complex waters without any subjective factors.