Based on energy balance principle, the energy response anlysis of the hybrid control system which is consisted of base-isolation and TMD is carried out, and the vibration control effectiveness of the hybrid control system under seismic ground motions with different pulse periods is studied. The Bouc-Wen model is adopted to simulate the isolation layer’s nonlinear force-deformation behavior. The motion equation and the relative energy balance equation are established. A eight-storey base-isolated structure is employed herein as an numerical example. The seismic response and energy response of the base-isolated structure with and without TMD are calculated using the fourth-order Runge-Kutta method and the trapezoidal rule, respectively. Input energy’s transformation and dissipation process of the hybrid control system are analyzed. Analysis results show that TMD’s control effect on the isolation layer’s peak displacement is not good. From the standpoint of the energy, TMD’s control to the input energy of the primary structure, especialy to the isolation layer’s hysteretic energy is very effective, and it’s the result of the energy dissipation by TMD’s damping. TMD shows different control effectiveness under seismic ground motions with different pulse periods, and the influence of the seismic grond motion’s characteristics should be considered when solving TMD’s optimum prameters.