Compared to theoretical models, finite element methods provide greater versatility for dynamic response analyses of rocking bridges, especially when considering the influences of various nonlinear boundary conditions. A finite element modeling method based on fiber section elements for three-dimensional seismic analyses of rocking bridges is developed in this paper. This method solves the problem of energy dissipation and stiffness determination of the rocking interface. Based on the proposed modeling method, considering nonlinear boundary conditions (such as abutment-soil interaction, impact effect, and pile-soil interaction), the seismic responses of rocking bridges, including free rocking, prestressed rocking and prestressed rocking with dampers, under the excitation of three-dimensional ground motions are analyzed. The results show that: after reasonable design, the prestressed rocking bridge with dampers exhibits similar seismic responses to the cast-in-place bridge, and maintains a good self-centering ability. The responses of all the rocking bridges under bi-directional loading are greater than those under unidirectional loading. In contrast, vertical ground motion's influence on the response of the rocking bridges is minimal. Ignoring the pile-soil interaction significantly underestimates the seismic demand of the evaluated bridges, especially the free rocking bridge and rocking bridge with prestressed tendons only.