Abstract: The classical groundwater seepage theory was established on the basis of the principle of water equilibrium, which cannot explain the phenomenon of well water level change caused by natural seismic activities and other external loads, and is not conducive to the in-depth understanding of the role of groundwater seepage movement in various environmental geological disasters. To solve this problem, a mathematical model of pore pressure change of a confined aquifer driven by seismic wave stress is constructed based on the fluid-structure coupling dynamic theory. The numerical verification of the model is realized by using the software Comsol. The change characteristics of well water level are inversely performed by using the Cooper theory, and the results are compared with the change characteristics of well water level caused by strong earthquakes in the Sichian-Yunnan region. The influencing factors of seepage movement of a confined aquifer under earthquake are studied by changing the simulation parameters. The results show that when seismic wave loads act on the confined aquifers, pore pressure oscillates in the same period as the seismic waves, and the amplitude, frequency and hydraulic slope of the seismic waves have significant effects on the pore pressure, while the coefficient of permeability and porosity have little effect on the change characteristics. At the initial stage of seismic wave loading, pore pressure increases rapidly, and then part of the water in the aquifer is slowly discharged. The load pressure gradually transfers to the granular framework, and the rate of change of pore pressure slows down and tends to reach a new equilibrium. The variation characteristics of well water level are closely related to pore pressure, and the oscillation period and variation pattern are consistent with pore pressure, but the amplitude is different. Generally, the oscillation rises and tends to be stable, which is basically the same with the variation pattern of well water level observed in the Sichuan-Yunnan region. The results are of valuable exploration significance for the establishment and improvement of groundwater seepage theory under stress, and can enrich and expand the research ideas and application fields of traditional groundwater dynamics and classical fluid-structure coupling theory.