In recent years, a study of a semi-active isolation system named the Leverage-type Stiffness Controllable Isolation System (LSCIS) was proposed. The main concept of the LSCIS is to adjust the stiffness in the isolator for the fundamental period of the superstructure by a simple leverage mechanism. Although great performance has been achieved with the support of the least input energy method (LIEM) in far-field earthquakes, some results still reveal that the proposed system is not suitable for application in near-fault strong ground motion. To overcome this problem, two algorithms that consider the potential energy effect in the semi-active structural control system are proposed in this study. The optimal weightings between the potential and kinetic energy are first determined through a series of near-fault earthquake simulations. The proposed algorithms are then developed with the combination of the potential energy (Ep) and the kinetic energy (Ep) as the control objective to reduce the structural displacement responses efficiently. In order to demonstrate the performance of the proposed algorithm, a two-degree-of-freedom structure is used as a benchmark in both numerical simulation and experimental verification. Numerical results have shown that the dynamic response of the structure can be effectively alleviated by the proposed algorithm under both far-field and near-fault earthquakes, while the structural responses by the LIEM may be worse than the pure passive control. The feasibility of implementing the proposed system has also been experimentally verified.