Abstract: In Xi'an city, the over-exploitation of groundwater is the most important factor for inducing land subsidence and ground fissures. The confined groundwater head increases the effective stress of the aquifer layer. The release compaction of cohesive soil water causes the land subsidence and ground fissures; it also results in the change of hydrogeological parameters, such as aquifer porosity, water storage coefficient and permeability coefficient. The borehole cores on both sides of the F4 ground fissure, served as the most active ground fissure in Xi'an city, are selected for the compacted CT scanning in this paper. Under the different pressures (head drawdown amplitude), the microstructure changes of the pores within 300m shallow clay have been obtained. And then, the coupling relationship between the permeability coefficient and microstructure change has been established. The results show that the large porosity and long porosity can decrease with the increasing pressure during the increase of soil stress caused by the groundwater exploitation. This is not conducive to the migration of water between pores. The macropores of the upper and lower aquifers of the ground fissure will decrease by 39.05% and 9.22%, respectively. The small and medium porosity is almost unchanged or only slightly increased. The permeability coefficient shows a decreasing trend with the increase of pressure. The aquifer permeability coefficient decreases with depth, the decline magnitude is gradually decreasing, and its maximum decrease is 71.08%. Thus, the research results have a guiding significance for scientific evaluation and prediction of land subsidence and ground fissure in Xi'an city.