Damping has a significant influence on the calculation of structural seismic response. In this paper, we compare the commonly used viscous damping (Rayleigh damping (RD) and Caughey damping (CD)) in combination with the isolated structure test. To avoid the arbitrariness of choosing two reference vibration frequencies in constructing RD, all the combinations of the first several vibration frequencies were calculated. Because the material characteristics of the isolation layer and the superstructure are significantly different and the deformation of the isolation layer is large, we construct nonproportional damping according to these two kinds of damping and make a comparative analysis. Analyzing experimental data, we can obtain the optimal frequency combination of RD and nonproportional damping during dynamic analysis of the isolated structure, the priority order of choosing damping models. For the calculation of RD, the 1st modal frequency of the structure should be included, and the 2nd and 3rd modal frequencies of the nonisolated structure are proposed to calculate the nonproportional damping based on Rayleigh damping (NP-RD) for the three-story frame structure in this paper. RD and nonproportional damping based on Caughey damping (NP-CD) are firstly recommended to be used in the calculation of the isolated structure, followed by NP-RD and then CD.