The mine–agriculture–urban compound area formed under the combined effects of natural conditions, mineral resource endowments, and historical development is affected by severe man-made disturbances, and faces a prominent contradiction between economic development and ecological protection. Guiding the future development is an urgent problem in this region. This research used image data, logical reasoning, and empirical analysis, based on social and economic statistics and land-use data, to analyze the typical characteristics and problems of the social–ecological system in the mine–agriculture–urban compound area. Moreover, we identified future directions for the region guided by policy documents and built a philosophy framework for sustainable development and management of the region based on the concept of adaptability. The results showed the following: (1) At present, the output value of the coal industry accounts for 84.10% of the total regional output value, severely disturbing its social–ecological system, which needs to be protected and restored under human guidance and management. (2) The future development of this region depends on the one hand on green mining, and on the other hand, it is necessary to fully tap the potential of arable land and livestock farms to develop efficient and intensive agriculture. (3) The key contents of the social–ecological system management of the mine–agriculture–urban compound area include resolving the contradiction between development and protection, ensuring development, optimizing industrial structure, and safeguarding public interests. In conclusion, this research can expand the connotation and application scope of adaptive management and provide a reference for such areas facing the prominent contradiction between development and protection.