Conventional isolation systems may induce an excessive response in near-fault earthquakes. A new short time Fourier transformation (STFT) control algorithm for variable friction dampers (VFD) is developed to improve the performance of base isolation buildings in near-fault earthquakes. The STFT controller varies the clamping force in the VFD damper to achieve the response reduction. In addition, the STFT algorithm is implemented analytically on a multi degree of freedom system (MDOF) with laminated rubber bearings and variable friction dampers in Simulink environment. Three types of earthquakes representing a wide variety of ground motions are considered as the ground excitations in the simulation. The numerical show that, compared with conventional isolation systems, the semi-active isolation system controlled by the STFT algorithm can reduce the excessive response in near-fault earthquakes effectively.