To investigate the evolution pattern of the regional groundwater cycle in an energy base in arid and semiarid areas of northern China under the influences of complex tectonics and coal mining, water samples from different aquifers in typical areas were collected, and the water levels of the major aquifers were observed. Hydrogeological analysis, hydrochemical tests (pH, total dissolved solids (TDS), anions and cations), hydrogen and oxygen isotopes (delta D, delta 18O) and an end-member mixed model were used to quantitatively identify the hydraulic connection characteristics of the aquifers under mining disturbance. The results showed that the independence of hydrogeological units in the study area is controlled by large deep faults;delta D, delta 18O revealed that the groundwater originates from atmospheric precipitation; the deuterium-excess (d-excess) of the Ordovician limestone aquifer (8.8 parts per thousand) is greater than that of the sandstone aquifer, and the isotope values of the mine drainage water are in between, confirming the mixing of sources. An end-member model showed that the contribution of Ordovician limestone water to the mine drainage water is 15.59%, and that of the No. 8 and 16 coal roof sandstone water is 84.41%, confirming that the Ordovician limestone aquifer recharges the coal-measure sandstone aquifer via hydraulic faults, and the water is drained by mining. This study elucidates the hydraulic connection evolution mechanism of "precipitation recharge-water conducted by tectonics-drainage due to mining" of karst groundwater in the study area and provides a quantitative basis for groundwater protection and mine drainage water disaster prevention and control in energy bases in arid areas.