Abstract: The sudden fluctuation in groundwater levels in granite (usually low in yield to wells) is influenced by the connectivity of fissures and precipitation. This phenomenon is abnormal that groundwater levels rose by more than 40 m within a day and returned to normal groundwater levels within a day after a few months. In this paper, more than 2 hydrologic years’ dynamic observation of the groundwater levels was Daya carried out in the ZK3 geological borehole in the Jiangmen Underground Neutrino Observatory near the Data Bay. Based on the hydrogeological conditions, geological structures, rock mass structures and the daily variation in rainfall in the study area, the reason for this specific phenomenon is analyzed. Shallow-dipping and steeply-dipping discontinuities with various orientations and lengths control the structure of the irregularity migration of groundwater. The distinctly differential groundwater transmissibility of the discontinuities at various depths before and after the rainy season is a significant factor contributing to sudden change in groundwater levels. In the rainy season, most of the surface runoff due to the underpart fissures is saturated with water, the surface runoff rate is high, the deep water is empty or is not saturated in the dry season, and the shallow water is easy to penetrate to the deep.