Karst water are important for water supply and ecological protection. However, climate changes and human activities have caused severe water supply crisis. The Jinci spring, one of the famous karst springs in China, is located at the basin‐mountain coupling belt and dried up since 1994. This study integrated hydrogeological conditions, water table logs, hydrogeochemistry, multiple isotopes, and numerical modeling to understand dynamic changes of interaction pattern between karst water‐Quaternary groundwater response to human activity in the basin‐mountain coupling belt over the past 60 years. Our investigation indicated that under natural conditions (1960s), karst water discharges as springs and laterally recharges into Quaternary groundwater at the fault area. In the 1980s, overexploitation caused a significant reduction in spring discharge and a decline in karst water levels, especially in coal mining areas. Further declines in water levels and mixing recharge by karst water‐Quaternary groundwater were observed in the 2000s, which were eased in 2018. Calculations both by oxygen isotope and models indicated that contribution of Quaternary groundwater to Jinci spring ranged from 11.8% to 42.1%, with the highest in the 2000s. Evidenced by multiple isotopes, the recharging of karst water‐Quaternary groundwater varied spatially along the belt in 2018, with delayed water level elevation in coal mining and heavy groundwater exploration areas. This study demonstrated that artificial disturbance fundamentally affected the karst water‐Quaternary groundwater flow and water exchange between them. Precautions should be taken when evaluating global water resources changes, in view of the dynamic interaction between the karst water‐Quaternary groundwater spatially and temporally.