Abstract: The carbonate strata overlying or underlying Paleozoic shales in South China are characterized by mutual development. High-quality shale layers are widely developed and widely distributed, and the recoverable resources of shale gas account for a large proportion. It is the main object of shale gas exploration and development in China. In the actual exploration, karst geological problems such as karst caves, fractures, underground rivers, confined aquifers and karst broken zones are easy to be drilled, which bring challenges to exploration and development and environmental protection. The oil and gas shale gas investigation team of Institute of Karst Geology, Chinese Academy of Geological Sciences has established the key technology of deep karst exploration for shale gas exploration in karst area based on years of exploration experience in karst area in southern China, which effectively serves the shale gas exploration in carbonate area in southern China.