Based on the research foundation of the existing equivalent model of multiple high-rise isolated structures, a dynamic response analysis method for the equivalent model of multiple high-rise isolated structures was proposed, which makes the structural response analytical solution have clear physical and engineering significance. For a simplified structure with two degree of freedom equivalent multi-layer isolation system, since the solution of the equation of motion of the multi-layer isolation structure using the strong vibration decoupling method that is widely used in practical engineering will produce large errors, the Kelly decoupling solution can greatly improve the accuracy of the solution. And for a three degree of freedom equivalent model of isolated high-rise structure, decoupling using strong decoupling method was used to analyze the error of the strong vibration decoupling method, and the results were corrected, which indicated that, the method of lifting the strong decoupling accuracy can also greatly improve the accuracy of the solution. Also, isolated structure with non-classical damping was analyzed for dynamic displacement response with standard second order oscillator to show that the existing seismic design method based on classical structure can be applied to isolated structures with non-classical damping characteristics. The method was demonstrated using example, the original multi-layer structure and the high-level structure were simplified into two degree of freedom and three degree of freedom models, respectively. The validity of the equivalent simplified model was verified by comparing the original structure with the equivalent simplified model. At the same time, the approximate decoupling solution method for non-classical damping isolation structures is simple and effective. With this method the dynamic response analysis of isolated structures becomes more complete.