Based on the theoretical analysis of the dynamic parameters of multi-DOF complex structures, it is shown that the optimum TMD parameters under the harmonic base excitation are not the exact optimization for seismic protection, whose main reason is that the optimum damping ratio of TMD for seismic protection is obviously lower than that under the harmonic base excitation. In this paper, an effective TMD design method is developed to control the seismic responses of many-degree-of-freedom complex structures. The EI-Centro seismic wave is introduced as the excitations and the approach to determining the optimum TMD parameters for seismic protection is effectively solved. Then with the case to design the TMD of a series reactor, the optimum TMD parameters for seismic protection are obtained. Its result proves that the designed TMD is able to reduce the seismic responses of the series reactor significantly, and this approach can provide a reference for the TMD design for seismic protection of other multi-DOF structures.