Abstract: Coal mining with high groundwater level causes a series of environmental geological problems, especially surface subsidence and subsidence waterlogging, that destroys a significant amount of cultivated land, damages the ecological environment and influences the sustainable development of coal resource-based cities seriously. To provide scientific basis for the ecological restoration of coal mining subsidence and subsidence waterlogging, three major problems need to be addressed: (1) How can the past spatial information of the subsidence waterlogging be reversed efficiently and accurately? (2) What are the spatio-temporal evolution characteristics of the subsidence waterlogging? (3) How to accurately predict the three-dimensional information of subsidence waterlogging? Therefore, this study first proposed a three-dimensional spatial information inversion method to obtain the past spatial information of subsidence waterlogging. The spatial information includes water depth, underwater bottom topography, water surface elevation, subsidence waterlogging area, and subsidence water volume. On this basis, the spatio-temporal evolution characteristics and main influencing factors of the subsidence waterlogging were analyzed. Finally, a three-dimensional spatial information prediction model the subsidence waterlogging was established. This study contributes significantly to provide the accurate spatial information of the subsidence waterlogging for waterlogging disaster prediction, ecological environment treatment, and restoration in coal resource-based cities with high groundwater level.