To investigate the effects of soil on the seismic energy response of the equipment-structure system, the shaking table test and the real-time substructure shaking table test of an equipment-structure-soil system were carried out in this study. The energy response of the equipment-structure system in the case of rigid ground was compared with those of considering the effects of soil. The input energy of the equipment-structure system was found to decrease significantly due to the effects of soil. Furthermore, the effect of soil led to a change in the time distribution characteristics of total energy input. Additionally, the energy response of the original equipment-structure system was also deduced based on the similitude scale factors, which resulted in significant errors compared with those of considering the effects of soil. Therefore, it is imperative to pay an attention to the effects of soil in the design of equipment-structure systems.