Abstract: Influenced by the carbonate facies and karst development degree, the types and characteristics of karst hydrogeological structures are different. Such a structural feature leads to variable pollutants in groundwater. In the shale gas development zone of Sichuan and Chongqing with widespread carbonate, the distribution of groundwater system and its cyclic evolution are more complicated. The identification of karst hydrogeological structure can provide effective guidance for the development and utilization of shale gas, and reduce or even avoid pollution of groundwater by shale gas development. Taking the area of Jiaoshiba-Luoyunba, a typical area of the Fuling shale gas exploration and exploitation zone in Chongqing as an example, this work studies the distribution characteristics of carbonate rocks, the development of karst and the occurrence and dynamic cycle of karst water in the shale gas exploration and exploitation area.Four types of karst aquifers, T1j-T2l, T1d, P2c-P2w and P1y, and the two types of concentrating and dispersing modes, are summarized. The system analysis method is used to extract four karst hydrogeological structures， gentle mono-slope, layered, anticline-folded multi-layer, and fault hydrogeological structures, of which the former two are of a pipeline-crack medium with smooth groundwater runoffs, prone to karst water pollution. In the latter two types of structures, the karst medium is dominated by crack networks with finite depth and extension, thus the distance and range of pollutant migration are small and the pollution capacity is limited.