Ancient brick pagodas reflect cultural exchanges, religious beliefs, historical changes and social-cultural influences. However, as a masonry building, it is composed of a typical brittle material exhibiting pronounced anisotropic properties. The material's tensile strength is significantly inferior to its compressive strength, which may result in substantial damage to the pagoda structure during seismic events. Simultaneously, the abrupt alteration in rigidity at the top of the ancient brick pagoda has resulted in a pronounced whipping effect, significantly endangering the integrity of the structure. Due to their inadequate anti-seismic protection, modern isolation technology is employed to safeguard ancient brick pagodas. The finite-element software ABAQUS is utilized to model ancient brick pagodas and perform time-history analysis. The results indicate that both horizontal and three-dimensional isolation technologies exhibit effective earthquake mitigation under the action of earthquakes. Horizontal isolation significantly reduces horizontal shear force, acceleration, and structural damage. Meanwhile, three-dimensional isolation further alleviates vertical axial force and vertical acceleration, thereby strengthening the structure's robustness. Additionally, both isolation techniques effectively mitigate the whipping effect of the pagoda spire. To sum up, isolation technology, especially three-dimensional isolation technology, can greatly improve the seismic performance of ancient brick pagodas and reduce the risk of damage and collapse during earthquakes. These studies provide a scientific basis for the anti-seismic retrofit of ancient brick pagodas and are of great significance for the protection of this type of cultural heritage.