Changes in the permeability of aquifers may have a significant impact on groundwater flow and thus on groundwater supplies and solute transport, while vertical permeability changes in aquitard may have an impact on the safety of underground waste repositories, aquifer vulnerability and may trigger seismicity. In a highly destructive tectonic activity, large earthquakes will cause different degrees of damage to the structure of well-aquifer system both in near and far filed, one of the most common phenomena is changes in permeability. Thus, quantitative evaluation of earthquake-induced permeability changes is important for understanding key geological processes. Many studies have independently documented permeability changes in either an aquifer or an aquitard, but the effects of an earthquake on both the aquifer and aquitard of the same well-aquifer system are still poorly understood. Analyzes show that well water level can be sensitive to response periodic loadings, especially to response earth tides and barometric pressures. And such response characteristics are closely related to hydraulic properties of the well-aquifer system. We investigated changes in aquifer and aquitard properties based on the water level response in a well in Zuojiazhuang (ZJZ), Beijing following the March 11, 2011, Tohoku earthquake. We employed a wavelet transform to capture the changes of the water level response in time-frequency space and combined tidal analysis and barometric response function to calculate earthquake-induced changes in the hydraulic properties of the well-aquifer system. Our results show that permeability increased both in the aquifer and aquitard after the earthquake. The horizontal transmissivity of the aquifer increased by a factor of six, and the vertical diffusivity of the aquitard doubled. This novel study highlights that large earthquake may threaten the groundwater flow system both in aquifer and aquitard.