With increasing global trade and frequent occurrence of disruptive events, the resilience of port clusters has emerged as a critical area of concern. However, studies that focus on the resilience of port clusters considering their complex network structure and operational dynamics remain limited. This study proposes a novel model to assess port cluster resilience by integrating hypergraph-based modeling and agent-based simulation. The model captures the complex relationships among ports and vessels, enabling the dynamic modeling of disruption impacts on port cluster resilience. A case study of the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) port cluster demonstrates the model’s applicability and effectiveness. Additionally, the significant impact of typhoon duration on resilience and the potential benefits of vessel port skipping behavior and port cargo handling capacity improvements are analyzed. These findings provide valuable insights for stakeholders in developing effective strategies to enhance the resilience of port clusters and the maritime transportation system.