The dynamic analysis model of multistage series non-proportion damping isolated structure is established.Citing partition of Rayleigh damping model,the non-proportional damping matrix of isolated structure is decomposed into the Rayleigh damping matrix and the surplus damping matrix reflecting non-proportional damping,and the damping matrix of multistage series non-proportion damping isolated structure is derived.Using the MATLAB software,the seismic respone analysis for a real structure is done.The results show that structure layer shear ration of the overall structure and peak displacement of isolation layer tend to correspond to value of base isolation as the lower structural mass and stiffness increased,when substructure has one layer and stiffness greater than 4 to 6 times of the upper structure stiffness of ground floor,it can approximately analyze as base isolation structure.