Aeolian dust emission is a major contributing factor to soil degradation and environmental pollution and threatens human well-being. Inner Mongolia, as an ecological barrier in northern China, is a hot spot of Aeolian dust emission, which indicates that the ecosystems act very important roles in preventing mineral dust from being emitted. In this study, utilizing a widely used model, we aim to identify the impacts of local ecosystems in preventing dust emissions and the corresponding trajectories in Inner Mongolia during 2001–2018. We found that the 18 years accumulated potential dust emission was approximately 12634.027 Tg, about ten times higher than the accumulated actual dust emission (approximately 1274.925 Tg); this showed the ecosystems of Inner Mongolia had prevented 11359.102 Tg mineral dust from being emitted. So, the prevention rate of the ecosystems was approximately 0.899. By studying the flow trajectories of ecosystems dust emission prevention (EDEP), we found that the EDEP worked most frequently in Spring and in the central regions of Inner Mongolia. The effects of EDEP mainly flowed to the areas located on the southeast of Inner Mongolia, like Shanxi, Hebei, Liaoning, Jilin, and Heilongjiang Province. We further identified the distributions of the EDEP benefiting areas and the corresponding beneficiary frequency. We found that the EDEP benefiting areas were distributed in most parts of China, and the regions closer to Inner Mongolia had the higher beneficiary frequency, especially the ones located in the eastern areas. This study provides some valuable theoretical foundations for the economic analysis of restoration projects.