Abstract: Carbonate rock is the main stratum in Fuling Area shale gas exploration and development area, and the underground fissures, karst caves and underground rivers are the important geological hidden dangers to be identified and prevented. In this paper, the characteristics of audio frequency magnetotelluric method(AMT) and shallow p-wave reflection seismic method are analyzed, it is considered that the method of electric shock combined with Fissure Cave survey is an effective way to obtain the corresponding relation between abnormal structure and resistivity and wave impedance. Through two application examples, this paper analyzes the occurrence law of strata, geological structure and fissure karst water in 500 m depth underground, the exploration result is reliable, and shows the research ability of integrated geophysical exploration on carbonate karst strata, it has promoted the development of geophysical prospecting for water in Karst water-scarce areas in southwest China, and made the basic geological survey widely used in shale gas exploration and development and long-term planning in Fuling Area.