To investigate the linkage mechanism between groundwater level dynamics and seismic activity across the hanging wall and footwall of fault zones, this study systematically collected the coseismic response characteristics of water levels in the Yining-2 and Yining-1 wells (located on the hanging wall and footwall of the western Kashi River fault, respectively) to moderate to strong earthquakes in the near and far fields. A comparative analysis was conducted on the relationships between the coseismic response rate/amplitude of the two observation wells versus the earthquake magnitude and epicentral distance and their coseismic response capabilities. Both wells exhibited oscillatory water level changes, and Yining-2 showed a greater coseismic response amplitude than Yining-1. Notably, 72.4% of recorded earthquakes originated from the hanging wall sector. Yining-2 also demonstrated a lower seismic wave energy density threshold for triggering a coseismic response and a superior linear correlation between the water level variation and magnitude/epicentral distance. The structural differences between the hanging wall and footwall of the thrust fault zone were significant. The hanging wall (Yining-2) featured a steeper fault dip angle, better-developed fractures, and closer proximity to the main fault, which created favorable hydrogeological conditions for rapid groundwater flow and recharge. In contrast, the footwall (Yining-1) displayed weaker hydrodynamic responses. The differences in the coseismic water level response were primarily controlled by local lithology and their tectonic settings rather than simple factors such as epicentral distance or earthquake magnitude. This study enhances the mechanistic understanding of coseismic water level responses and provides critical insights for optimizing fluid monitoring well networks.