The ecologically fragile region in China and Mongolia is among the regions with the largest distribution area, the largest type of fragile ecology, and the most evident ecological vulnerability. The ecological environment condition in the ecologically fragile areas of China and Mongolia restricts the sustainable development of regional ecology and social economy, and is crucial to the ecological security of China and Mongolia. Thus, it is urgently necessary to thoroughly explore the characteristics of ecologically fragile ecosystems in China and Mongolia and their response mechanisms to global changes, which can provide a scientific basis for regional ecological environmental restoration. Based on the carbon and nitrogen cycles of fragile ecosystems affected by global change, this study presents and summarizes the following key research topics: fragile ecosystem carbon and nitrogen cycles and coupling mechanisms, the influence of global change on fragile ecosystems, fragile ecosystem safety threshold identification and risk assessment under the background of global change, and the adaptive management of fragile ecosystems to global change. In view of the national major needs of ecological safety, researches in the following aspects are urgently needed: analyzing the annual, seasonal, and diurnal characteristics of nitrogen turnover pathways, transformation form, and flux in water-soil-gas-biomass systematically to reveal the carbon and nitrogen cycling process, spatio-temporal law, and coupling mechanism of fragile ecosystems and determine the primary mechanism of the carbon and nitrogen sink function in fragile ecosystems. Building a carbon and nitrogen coupling model in fragile ecosystems, quantifying the influence strength of different intensities of climate change on fragile ecosystem safety and the influence of human disturbance on the carbon and nitrogen cycle and its ecological system, assessing the effect of fragile ecological systems on the carbon and nitrogen cycle in the Earth system and its carbon and nitrogen source-sink effect, and proposing management countermeasures and measures of fragile ecosystems to global change.