The Yellow River Basin is also known as China’s energy basin. Rational and orderly exploitation of mineral resources and overall coordination of the relationship between mineral resources exploitation and ecological environment protection are of great practical significance for the sustainable development of energy and mineral resources and ecological protection in the region. Taking the Yellow River Basin as the study area, this study comprehensively analyzed the characteristics and spatial distribution of environmental stress of regional mineral resources exploitation using multi-indicator comprehensive evaluation method, stress coupling analysis method, and GIS spatial analysis from the perspectives of ecological background fragility, spatial stress to important ecological function areas, and the degree of stress to important ecological environment factors. The 46 mining cities in the Yellow River Basin were divided into eight types, including background stress areas, ecological function stress areas, development stress areas, background with development stress areas, development with ecological function stress areas, background with ecological function stress areas, comprehensive stress areas, and no stress areas. Finally, the article put forward the control path of mineral resources development areas in the Yellow River Basin in view of ecological environment protection, including: (1) Spatial management and control by strictly restricting large-scale and high-intensity industrialization and urbanization development, especially controlling the development boundary of mining areas. (2) Intensity control for areas with fragile ecological background, the intensity and the overall development scale should be controlled simultaneously. (3) Development mode control to pay attention to the structural adjustment and upgrading of energy and mining industries. It is necessary to focus on spatially concentrated development of mining in places where mining is suitable, of industry where industrial development is suitable, and of cities and towns where urban development is suitable.