The upper Yellow River is the most important water conservation area as well as the runoff and confluence area in the Yellow River Basin, and accounts for more than half of the runoff of the entire basin. Therefore, it is of great significance to the ecological protection, water resource security, and food security of the entire Yellow River Basin. Scientifically understanding the change characteristics of natural environmental factors and deeply exploring the coordination problem of natural environmental factors can promote ecological protection and high-quality development of the Yellow River Basin. Based on the macro understanding of the six important characteristics of natural environmental elements, such as climate, hydrology, and ecology, in the upper Yellow River under the background of global warming and the implementation of national ecological protection projects and water resource management policies, this study describes the natural disharmony among hydrology, soil, climate, and ecology in the upper Yellow River. Moreover, from the perspective of the coordination of natural environmental elements, this study puts forward five scientific ideas on how to eliminate the traditional thinking and misunderstanding of ecology and development problems in the upper Yellow River, as well as six scientific suggestions on how to build an ecological protection and high-quality development model with regional characteristics. This study has important guiding significance for the promotion of ecological protection and high-quality development of the upper Yellow River.