Water and land resources are important material bases of economic and social development, and their spatial patterns determine the pattern of the urban development. The development and expansion of coal-resource-based cities have introduced new societal problems, such as the overlapping of new city construction areas and underground coal resources. Underground coal mining also leads to surface subsidence, which destroys water and land resources and seriously affects the sustainable development of coal-resource-based cities. The surface subsidence area takes a long time to stabilize, and may form a large waterlogging area due to the high groundwater level, thereby increasing the difficulty of reconstructing mining subsidence areas. In this context, a scientific and complete method for reconstructing the spatial pattern of water and land resources in unstable coal mining subsidence areas within urban is proposed in this paper. This method initially predicts the surface subsidence value and then divides the subsidence area within the urban region into the waterlogging area and the non-waterlogging area according to the surface subsidence value. The waterlogging area will be renovated into a landscape lake district in the city by a series of transformation measures. Afterwards, goaf rock mass activation and surface stability evaluation analyses are performed in the non-waterlogging area. According to the evaluation results, land resources can be divided into unaffected, restricted and prohibited building areas, with each area being transformed differently. The Lv Jin Lake in Huaibei is selected as a case study, and the proposed method is applied to reconstruct its water and land resources. The original spatial pattern of the large-scale waterlogging area and abandoned land due to mining subsidence in urban areas is then reconstructed into a spatial pattern that integrates the urban landscape, scenario living and eco-tourism. Compared with traditional subsidence area management, the proposed method greatly increases the utilization value of water and land resources, improves the urban ecological environment, enhances the urban quality and effectively alleviates the problems of land shortage and human–land conflict in coal-resource-based cities.