An essential component of waterborne cargo movement is ship pilotage. This study offers a risk assessment model based on the Work Breakdown Structure-Risk Breakdown Structure (WBS-RBS) and cloud model to evaluate and control the risks during the full process of ships entering and leaving port. To thoroughly identify the risk elements at every stage of ship pilotage, utilize the WBS-RBS. The primary risk factors are identified using the Technique for Order Preference by Similarity to an Ideal Solution (TOPSIS). The comprehensive weights of the risk factors are obtained using the Analytic Hierarchy Process (AHP) and The Criteria Importance through the Inter-Criteria Correlation (CRITIC) approach. The risk assessment is then conducted using the cloud model. A case study of Qinzhou Port is conducted to assess the risks throughout the entire pilotage process. The results show that the risk level of pilotage in Qinzhou Port is medium. For ships entering Qinzhou Port, the preparation stage and the stage of completion and reporting are low-risk, while the coordination & communication and pilotage operation stages are medium-risk. This paper provides a reference for ship pilotage risk assessment research and a theoretical basis for safety management departments to develop risk control measures.