Abstract: Taking Qidong Coal Mine as an example, this paper studies the law of groundwater migration and the characteristics of structural water control in the region, in order to provide reference for advanced precise control and regional prevention of coal mine water disasters. Based on the theory of structural water control and combined with the geological and structural background of Qidong Coal Mine and its mining area and coalfield, the step-by-step control effect of structural water control and the mode of structural water control are studied. The results are as follows: The bedrock formation morphology of Qidong Coal Mine is controlled by Sunan syncline as a whole, partly by Weimiao fault and other structures, and the Cenozoic formation morphology is also indirectly controlled by structures. Under the control of Sunan syncline, Permian coal-bearing sandstone fractured aquifer, Taihui, Ordovician limestone and aquifer IV angle unconformity contact after weathering inside or outside the mine; under the control of Weimiao fault, the aquifer of partial Permian coal-bearing sandstone fractured aquifer in the southern mining area of the mine outcrops again, and contacts with the aquifer IV angle unconformity, which makes the hydraulic connection between the aquifers. Based on the analysis results, it is considered that ① the geological structure controls the underground aquifer water by controlling the formation morphology ; ② Geological structure controls the hydraulic connection between aquifers by controlling the contact between aquifers. In order to further verify the hydraulic connection between aquifers, using the comparative analysis of water level changes and Pearson correlation coefficient, the borehole water level observation results of aquifer IV, Taihui and aquifer IV, Taihui and Ordovician limestone in the southern mining area during the water discharge test and normal water level observation period were analyzed. The results show that: ① During the water discharge test in the southern mining area, the water level changes of aquifer IV (SQ10-14) and Taihui (ST4) are basically synchronous and highly correlated; ② During the normal water level observation, there is a strong correlation between the water level changes of aquifer IV (SQ10), Taihui (ST4) and Ordovician limestone (SO2), and the correlation between different observation holes in the same aquifer is quite different. It is confirmed that, controlled by the structure, there is hydraulic connection in the angular unconformity contact area between the fourth aquifer and the bedrock aquifer in the local area of the mine. The groundwater model system (GMS) and parameter estimation (PEST) are used to study the distribution and runoff law of four water levels. The results show that the four water levels are about−7−−57m, the water level in the south is higher than that in the north, and the hydraulic gradient is larger at the Weimiao fault. The four water-bearing runoff is concentrated in the southwest and central part of the mine. The southwest runoff is northward as a whole, and the central part is mainly east-west runoff. The four water-bearing runoff bypasses the Weimiao fault.