This paper aims to develop a system to control the vibrations of ancient pagodas without damaging their original appearance. Taking the Small Wild Goose (SWG) Pagoda (Xi'an, Shaanxi Province) as the target structure, the authors designed a shape memory alloypendulum damping system (SMA-PDS) based on the theory of pendulum damping and the super elasticity of the SMA. To verify the effect of the SMA-PDS, a 1:10 scale model was created for the SWG Pagoda, and subjected to shaking table tests with and without the SMA-PDS. The test results indicate that: the small and flexible system can be installed easily inside the pagoda to dampen seismic vibrations; the SMA-PDS greatly reduced the acceleration response at the top of the SWG Pagoda model; the reduction is particularly prominent (32.5%), when the SMA wires had a pre-strain of 3%; the SMA-PDS worked better in medium and large earthquakes than in small earthquakes. To sum up, this paper provides a novel damping system for seismic vibration in ancient pagodas, shedding new light on the energy dissipation, vibration control and reinforcement of similar ancient pagodas.