A model of equipment structure coupling isolation system was first established in this paper, then fifty near fault pulse like and fifty near fault non pulse like seismic waves were selected to determine the dynamic responses of the isolation system. The analysis results show that the effect of near fault pulse like ground motions on the coupling isolation system is greater than that of near fault non pulse like ground motions, and the effect on the main structure is greater than that on equipment. Average responses of the displacement of isolation layer, story drift, floor acceleration, equipment acceleration, and equipment displacement under near fault pulse like ground motions are 2.25 times, 2.17 times, 2.24 times, 1.17 times, and 1.20 times of those under near fault non pulse like ground motions, respectively. In the design of the equipment structure coupling isolation system, the impact of pulse characteristics of near fault ground motions should be considered. Meanwhile, it should be noted that ground motions causing the maximum response of the main structure and equipment may not be the same.