Abstract This paper adopted organic components, environmental isotopes, and organic components to study water quality comprehensively, in order to distinguish the differences of hydrogeochemical characteristics between coal measure strata and aquifers on the roof of deeply buried mining areas in Inner Mongolia-Shaanxi, China. The results show that the deeply buried mining area in Inner Mongolia-Shaanxi belongs to Mu Us Desert, and the surface is covered by aeolian sand, with excellent precipitation infiltration capacity. Salinity of surface water and Quaternary water<500 mg/L, the main cation is Ca2+, and the main anion is HCO3-, which belongs to HCO3-Ca·Mg type water. The Cretaceous Zhidan Formation is in unconformable contact with the Quaternary and constitutes a unified water-bearing complex on the whole, which makes Zhidan Formation have a better supply water source, and its inorganic water quality characteristics are close to the Quaternary water. The deep aquifer is affected by the Anding Formation relative impermeable layer and has weak recharge runoff condition. The salinity of Jurassic water is generally >3500 mg/L due to long-term water-rock action. The main cation is Na+, and the main anion is SO42-, which belongs to SO4-Na type water. According to the analysis of hydrochemical characteristics, there is no direct hydraulic connection between Luohe Formation and Zhiluo Formation. The characteristics of environmental isotopes show that the rainwater, surface water, and Quaternary water in the study area belong to the modern groundwater, while Zhidan Formation water is between the modern groundwater and the ancient water. The values of δD and δ18O in the deep Zhiluo Formation and Yan’an Formation are low, and the groundwater falls below the rainwater line of Ordos Basin with a deep circulation depth. Before mining, the groundwater is in a stagnant state with good closed conditions. Qualitative and quantitative signatures of various organic components in water are on the basis of organic geochemistry and hydrogeology, in order to facilitate the study of the quantity, composition, and distribution patterns of organic substances in groundwater and their role in geological, geochemical, and other processes. By testing the organic matter of dissolved organic matter (DOM) in each aquifer, the organic water chemistry characteristics of each aquifer in the Taokutu well field can be established. The content of dissolved organic matter (TOC and UV254) in groundwater decreases gradually with the increase of aquifer depth. Fluorescence peaks in Area I and Area III mainly appeared in surface water and Quaternary water, and DOM sources were more abundant in surface water. The fluorescence peak in Area I also appears in the water of Zhidan Formation, Zhiluo Formation, and Yan’an Formation, and the fluorescence peak between Area I and Area II is a symbol. The fluorescence peak intensity of Cretaceous → Zhiluo Formation in Area V area has an increasing trend, indicating that there are humus-like DOM from other sources in the deep Zhiluo Formation aquifer. In general, the comprehensive analysis of hydrochemical characteristics by various means can well distinguish the differences of hydrogeochemical characteristics among aquifers, which provides a scientific basis for the rapid and accurate discrimination of water situation and disaster in coal mines and the safe production.