Based on the suspension damping principle and the superelasticity of shape memory alloy （SMA）， the shape memory alloy compound suspension damping system （SMA-SPDS） is developed. The Matlab/Simulink simulation model of SMA-SPDS is established， a 1/10 scale model of Xiaoyan Pagoda structure is simulated and analyzed. After verifying and analyzing the values of simulation analysis and shaking table test results， the optimal setting of the prototype structure of Xiaoyan Pagoda is carried out， and the damping analysis of the prototype structure of Xiaoyan Pagoda is further carried out by using this method. The results show that SMA-SPDS can improve the integrity of the prototype structure and enhance the seismic performance of Xiaoyan Pagoda prototype structure； SMA-SPDS has an obvious effect on reducing the seismic response of Xiaoyan Pagoda structure， and with the increase of seismic intensity， the damping effect is more obvious， especially for the control effect of the inter-layer displacement angle， the displacement angle of the lower layer can be reduced by more than 50% under the large earthquake； The simulation model of Xiaoyan Pagoda can better reflect the real situation of its prototype structure and verify the feasibility of the simulation analysis method， which can provide a reference for seismic protection of similar ancient pagoda structures.