The risk caused by different environmental factors in the navigation of ships is not uniform. The univariant (e.g., sea fog), covariant (e.g., wind and waves), and spatially restricted (e.g., offshore distance) risk factors present a complex non-linearity impact on the navigation of ships. This means that a comprehensive evaluation of the environmental risk for navigation should consider the risk characteristics of different factors. In this paper, a non-linear spatial multi-criteria decision (SMCD) method-based evaluation framework was developed to evaluate the potential environmental risk of navigating ships. (1) Non-linear weight adjustment and risk decision functions were proposed to spatially evaluate the comprehensive risk and avoid diluting the critical impact of high-risk factors. (2) The double thresholds standardization approach was developed to construct the risk association between different tonnage ships and environmental factors. (3) The developed methods were used in the Bohai and Yellow Seas as a case study to verify the validity and practicability. The quantitative analysis, historical accident matching (82% accident matching rate), and a real accident case proved the validity of the developed model.