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Current methods account for control–structure interaction (CSI) in structural control design, which may be unavailable in the preliminary design phase of actively controlled structures due to the unknown dynamic characteristic of an actuator. Therefore, it may result in significant difference in the design and evaluation of an active structural control system when ignoring or considering CSI at different phases. To eliminate the CSI effects of electromagnetic mass damper (EMD) system and thus decouple the tracking control of EMD from the control design of structure, in this paper, an improved three-variable control (ITVC) combining a signal convertor, a typical three-variable controller, and a voltage compensator is developed. The voltage compensator counteracts the influence of lower-order CSI including viscous damping force and Coulomb friction. The three-variable controller reduces the higher-order CSI effects, while the signal convertor converts all command and feedback signals to the relative coordinate system and eliminates the additional CSI effects. Performance tests and frequency response tests of the EMD system show that the CSI effects are basically eliminated by ITVC. In addition, shake table tests are performed on a one-story actively controlled structure to further verify ITVC. Experimental results suggest that ITVC can apply accurate control force on the structure and achieve ideal structural response control.