In order to protect a structure over its full life cycle, a novel tuned mass damper (TMD), the so-called semi-active eddy current pendulum tuned mass damper (SAEC-PTMD), which can retune its frequency and damping ratio in real-time, is proposed in this study. The structural instantaneous frequency is identified through a Hilbert-Huang transformation (HHT), and the SAEC-PTMD pendulum is adjusted through an HHT-based control algorithm. The eddy current damping parameters are discussed, and the relationship between effective damping coefficients and air gaps is fitted through a polynomial function. The semi-active eddy current damping can be adjusted in real-time by adjusting the air gap based on the linear-quadratic-Gaussian (LQG)-based control algorithm. To verify the vibration control effect of the SAEC-PTMD, an idealized linear primary structure equipped with an SAEC-PTMD excited by harmonic excitations and near-fault pulse-like earthquake excitations is proposed as one of the two case studies. Under strong earthquakes, structures may go into the nonlinear state, while the Bouc-Wen model has a wild application in simulating the hysteretic characteristic. Therefore, in the other case study, a nonlinear primary structure based on the Bouc-Wen model is proposed. An optimal passive TMD is used for comparison and the detuning effect, which results from the cumulative damage to primary structures, is considered. The maximum and root-mean-square (RMS) values of structural acceleration and displacement time history response, structural acceleration, and displacement response spectra are used as evaluation indices. Power analyses for one earthquake excitation are presented as an example to further study the energy dissipation effect of an SAECPTMD. The results indicate that an SAEC-PTMD performs better than an optimized passive TMD, both before and after damage occurs to the primary structure.