An interactive numerical calculation method to simulate the real-time substructure shaking table testing for the equipment-high rise structure-soil system was proposed. Considering that the soil is not completely nonlinear under strong earthquakes, locally nonlinear soil model was adopted as the numerical substructure in order to consider the influence of nonlinear soil during the substructure testing. Meanwhile, the equipment-high rise structure system was adopted as the experimental substructure. Then, equations of motion for the equipment-high rise structure-locally nonlinear soil system was derived using the branch modal substructure method and the linear-nonlinear hybrid constraint modal substructure method. A thirteen-layer steel framework system model was used as an analytical example, that the equipment-high rise structure system and locally nonlinear soil computing model were built by MATLAB and ANSYS respectively. Data communication occurred between two parts. Through the numerical result, it is found that the soil-structure interaction(SSI)and the frequency change of equipment have important influences on the seismic response of equipment and structure.