Permafrost is widespread in China, especially in Northeast China and the Qinghai-Tibet Plateau. Regions like Qinghai-Tibet Plateau have the most strenuous crustal movement. Therefore, earthquake-resistance of structures in permafrost region is an important issue. Furthermore, the permafrost will degenerate gradually as global warming mounts up. In some regions permafrost thickness tends to attenuate. Most bridge designs adopt pile foundation in order to reduce the effects of instable frost. The deterioration of frost leads to degradation of anti-seismic performance of bridges’ pile foundations. Pile-soil dynamic interaction numerical analysis models are established based on data of indoor low-temperature dynamic triaxial tests. Studies are performed on the dynamic stiffness and damping characters and the influencing factors of pile foundation under vertical harmonic load in frozen and thawing soil. The result shows that the dynamic response of the pile decreases along the depth, and the frictional resistance around the pile mainly distributes along the upper half of the pile, and the dynamic stiffness and damping of the pile are affected by temperature. Dynamic stiffness increases as temperature goes down, whereas the decrease of the temperature of frozen soil can notably lower the dynamic damping of the head of the pile. As the frequency of the dynamic load augments, the dynamic stiffness of the head increases marginally, whereas frequency has little influence on damping. The relative thickness of the frozen and thawing soil layer has considerable influence on dynamic stiffness, but negligible on damping.