Hypogene karst is a special manifestation of karst development in spatial scale. Intensive study of its development mechanism has significant meaning for engineering construction, shale gas and geothermal exploitation. To reveal the developing pattern of hypogene karst in Huanjiang syncline, karst groundwater at different depths in wells HD1-2 and HD1-4 and karst springs was selected as the research object. Through the analysis of geochemistry and stable isotopes of karst groundwater, it was revealed that the circulation pattern of deep karst water came from the common recharge of meteoric water and fossil water hosted in karst caves, runoff of deep faulting belts and discharge of large karst springs, over Huanjiang syncline, which provides good hydrodynamic conditions for hypogene karst development. Meanwhile, the widely developed faulting belts and structural fissures provide primitive dissolution space. Through the above analysis, the paper constructs a hypogene karst development pattern controlled by the deep cycle of groundwater in Huanjiang syncline.