In cold and high-intensity seismic regions, such as the Qinghai-Tibet Plateau in China, the deterioration of material properties caused by freeze-thaw cycles and permafrost degradation due to climate change have become increasingly severe, posing significant challenges for the seismic performance assessment of bridge pile foundations. To systematically investigate the impact of permafrost degradation and material freeze-thaw deterioration on the seismic performance of bridge pile foundations and ensure proper seismic design, a pile-frozen soil interaction finite element model was established, considering both permafrost degradation and material freeze-thaw deterioration. A comparative analysis was conducted to evaluate the influence mechanisms of various factors on the seismic performance of bridge pile foundations in permafrost regions. The results indicate that as the bridge service life increases, the horizontal bearing capacity, equivalent stiffness, and energy dissipation capacity of the pile-frozen soil system all show a decreasing trend. Notably, the combined effect of permafrost degradation and material freeze-thaw deterioration has a more significant impact on the seismic performance of the bridge pile foundation. Specifically, after 100 years of bridge service, the horizontal bearing capacity of the pile-frozen soil system reduces to approximately 55% of its initial value, whereas when only permafrost degradation is considered, the horizontal bearing capacity drops to around 89% of its initial value. Therefore, neglecting the effect of material freeze-thaw deterioration would lead to an unsafe seismic performance assessment of the bridge pile foundation. In the seismic performance analysis of bridge pile foundations in permafrost regions, it is essential to consider not only the effect of permafrost degradation but also the impact of material freeze-thaw deterioration.