To reduce the effects of earthquakes on the ancient Small Wild Goose Pagoda, a shape memory alloy-suspension pendulum damping system (SMA-SPDS) is developed by combining superelastic SMAs with damping pendulum theory. A MATLAB/Simulink simulation model of the SMA-SPDS is established and tested on a 1:10 scale model of the Pagoda. After verifying and comparing the simulation data with experimental results, a shock absorption analysis is performed on the prototype Pagoda. The optimum engineering design for the prototype structure of the Small Wild Goose Pagoda using SMA-SPDS for shock absorption protection in the future is put forward. The results show that the performance of the SMA-SPDS system is stable, and it can improve the integrity of the original structure of the Pagoda for better performance during earthquakes. In addition, with an increment in seismic intensity, the SMA-SPDS shows an apparent controlling effect. The Simulink simulation results of the model structure of the Small Wild Goose Pagoda are in good agreement with the test results. The Simulink simulation method can simulate the seismic response of the model structure of the Small Wild Goose Pagoda well, with and without SMA-SPDS, to obtain a more real damping effect of setting SMA-SPDS on the prototype structure; the engineering optimization of the location, quantity, and system performance parameters of SMA-SPDS in the prototype structure of the Small Wild Goose Pagoda has a remarkable effect, which can make the damping effect of SMA-SPDS reach more than 43% floor.