In the context of global climate change and rapid urbanization, enhancing flood resilience is essential for mitigating urban flood risk. However, few studies have conducted long-term, cross-scale dynamic evaluations of flood resilience and analyzed its influencing factors and mechanisms. Taking the Beibu Gulf urban agglomeration as the study area, a long-term, cross-scale dynamic evaluation index system based on the “Robustness-Resistance-Recovery” (3Rs) framework was developed to assess the spatiotemporal evolution of flood resilience from 2000 to 2020. Furthermore, the optimal parameters-based geographical detector model is employed to identify the key influencing factors and mechanisms. The results reveal that pre-flood robustness is lower in coastal areas and higher in inland areas. In the during-flood stage, cities with greater comprehensive power exhibit stronger resistance. Post-flood recovery is higher in city centers and marginal mountainous areas, while coastal and inland low-lying areas show lower recovery. The flood resilience of urban agglomerations has improved in recent years, largely due to the enhancement of urban flood control infrastructure and healthcare capacity. However, disparities between cities persist. From 2000 to 2020, economic factors have been the primary drivers of improved flood resilience, while ecological factors have gained increasing importance over the past decade. These findings provide valuable insights for flood prevention, mitigation, and resilience management in urban agglomerations. The developed dynamic evaluation index system offers a reference framework for evaluating flood resilience in other regions.