The energy equations of the base-isolated structure are established based on the energy equilibrium theory. Reasonable strong seismic motion records are selected. Based on the general FEA program, the bidirectional nonlinear behavior of lead rubber bearing is taken into account by using two orthogonal nonlinear spring elements. Considering the effect of principal parameters of lead rubber bearing and dissimilar seismic motions, dimensional FEA model of base-isolated structure is established. And the seismic energy response analyses for base-isolated structure are carried out under the three-dimensional seismic motions. The study results are obtained as follow: 1) With the increment of lead core diameter or stiffness ratio, the seismic input energy can be enlarged and the isolation effect of lead rubber bearing can be reduced; 2) The seismic energy response of base-isolated structure is greatly discrepant under different seismic motions. Especially, when the duration of seismic motion prolongs or the natural period of base-isolated structure approaches to the predominant period of seismic motion, the seismic energy response of structure can be enhanced.