Based on branch substructure method, this article deduces motion equation of an equipment–structure–soil interaction system. The equation is converted and applied to a shaking table real-time substructure experiment. The equipment–structure system is adopted as experimental substructure loaded by the shaking table. Meanwhile, finite element model of soil is adopted as numerical substructure after modal reduction. An equipment–structure–soil interaction scale model is designed and tested using shaking table under different earthquake records. Comparison shows good agreement of results of experimental and finite element methods. This work also proves validity and accuracy of the proposed experimental method.