The purpose of this study is to provide safety pre-warning and guarantee for the transportation of hazardous chemicals in transport enterprises. To this end, this paper conducts a risk assessment study on hazardous chemicals transportation based on fuzzy comprehensive evaluation (FCE) method. Taking the waterway transportation of transport enterprises as the research object, the fuzzy analytic hierarchy process (AHP) was selected and used to establish secondary index evaluation system from five aspects: transportation equipment, hazardous chemicals, man, transportation environment and enterprise management. Also, the analytic hierarchy process (AHP) was applied to configure the index weights. Thus, a fuzzy comprehensive risk assessment model for hazardous chemicals was established. The example analysis results show that the fuzzy risk assessment model can quantitatively evaluate the risk level of hazardous chemicals transportation. The risk score of a transport enterprise in Zhoushan is 66.2, which belongs to the general safety level with potential transportation risks. This provides effective theoretical guidance for risk assessment and orientation reform of hazardous chemicals transportation enterprises.