Abstract: Water conservation and coal mining are both critical to Northwest China. Water conservation-based coal mining is an important technology for the coordinated development of coal and water resources in this region. In this technology, the evaluation of aquiclude stability is critical. Due to the shallow depth of coal seams, intense topographic cutting, and complex changes in near-surface aquifers in the ecologically vulnerable areas in Northwest China, there exist large errors between traditional methods for aquiclude evaluation and the actual hydrological observations in these areas. To address this challenge, this study develops using the 3D geological modelling combined with numerical simulation to accurately evaluate the aquiclude stability in the water preservation-based mining of shallowly buried coal seams. First, an intuitive and reliable 3D geological model is constructed based on the exploration information and topographic contour maps. The purpose is to finely characterize topographic cutting and the complex changes in shallow aquifers. Then, numerical simulations of damage to the rocks overlying coal seams are performed by selecting several typical mining faces, aiming to determine the heights of the hydraulically conductive fissure zones at various coal seam points in the 3D model. Finally, using the 3D geological block model, the differences between the heights of the hydraulically conductive fissure zones and the thicknesses of overburden rocks’ aquifers were calculated for various coal seam proof points from the full 3D angle. These differences were employed to evaluate the aquiclude stability in water conservation-based coal mining. This study investigated the Mandura coal mine in Ordos. Based on the collected stratigraphic columns of 36 boreholes in the coal mine and its topographic and geological maps, this study established a fine-scale 3D geological model and evaluated the aquiclude stability. As indicated by the comparison of the observations of two underground waterlogged areas in the Mandura coal mine, the unstable aquiclude zones calculated using traditional methods failed to accurately reflect the area filled with water on the southern mining face. In contrast, the unstable aquiclude zones calculated using the new method was more fine-scale, adequately reflecting the effects of topographic cutting, weathering, and denudation on the Quaternary aquifers. As indicated by the results of this study, compared to traditional evaluation methods, the method for evaluating the aquiclude stability of shallowly buried coal seams based on 3D geological modeling can characterize the effects of the mining of shallowly buried coal seams on aquifers more intuitively and accurately and exhibits higher adaptability. Furthermore, the new method can provide fine-scale evaluation indices for water preservation-based coal mining.