The pile group-pile cap structure is a key foundation form for deep-water bridges. However, current effective methods for calculating the earthquake-induced hydrodynamic forces on pile caps with arbitrary cross-sections remain insufficient. In this study, the hydrodynamic force is considered as the added mass, and the dynamic equilibrium equations of the isolated pile cap structure (IC model) and the pile group-pile cap structure (PC model) under earthquakes are established, respectively, based on the structural dynamics theory. Correspondingly, the relationships between the hydrodynamic added masses and the fundamental frequencies in the IC model and the PC model are derived, respectively. The fundamental frequencies of the IC model and the PC model are obtained by numerical models built with the ABAQUS (2019) finite element software, and then the added masses on the IC and PC models are calculated accurately. The calculation method proposed in this study avoids the complex fluid–structure interaction problem, which can be applied for the seismic design of deep-water bridge substructures in real practice.