This study introduces an offline iteration-based real-time hybrid simulation (OI-RTHS) method, a novel approach for simulating fluid–structure dynamic interaction (FSDI) under seismic excitation. With this method, hydrodynamic forces are treated as a physical substructure, while numerical computation and servo loading are performed independently throughout the entire duration of the seismic event. By iteratively correcting the input command signals and obtaining the output response signals during each iteration process, they can eventually achieve balanced coordination at the boundaries. This characteristic introduces real hydrodynamic data to address the limitations of purely numerical theoretical analysis, ensuring high fidelity. Additionally, it reduces the need for real-time communication between numerical computation and servo loading, thereby reducing hardware and software requirements. In this study, experimental verification of the proposed method is conducted, and the results illustrate that the method can address the convergence issue of dynamic response for FSDI of structures in the water after a finite number of iterations. Moreover, regarding the hydrodynamic force as a physical substructure helps prevent errors arising from repeated loading processes, enabling the benefits of the OI-RTHS method. This study offers potential insights for the research on the FSDI of structures, also other environmental loadings.