[Objective] To investigate the influence of land use change patterns on the spatial distribution of carbon sinks in the Inner Mongolia section of the Yellow River Basin, and to identify the main driving factors behind, so as to provide a basis for ecological spatial development directions and sink enhancement policies in the study area.[Methods] Taking the Inner Mongolia section of the Yellow River Basin as an example, we used the InVEST-FLUS model to analyze the changes of carbon sink capacity in each period based on land use data in 2000, 2010 and 2020, and simulated the patterns of carbon stock changes in 2040 under three different scenarios of natural development, ecological conservation and agricultural priority, and identified the factors behind the differences in the spatial distribution of carbon sinks with the help of geographic probes. The main driving factors behind the differences in spatial distribution of carbon sinks are identified with the help of geographic probes. [Results]① From 2000 to 2020, carbon storage in the Mongolian section of the Yellow River Basin increased first and then decreased, with an overall increase of 8.63×106t, in which subsurface biological carbon storage increased by 3.91×106t and soil carbon storage increased by 2.28×106t. ②Carbon storage continued to decrease by 3.92×106t in the future natural development scenario, but increased by 22.1×106t in the ecological protection scenario, which was higher than that of 4.99×106t in the agricultural priority scenario. Soil carbon storage was the key to the incremental difference. ③The unbalanced distribution of annual mean rainfall and annual mean temperature is the main factor that causes the difference of various carbon pools in the Mongolian section of the Yellow River Basin. [Conclusion] Reasonable ecological protection policies are more in line with the future requirements of urban intensification and ecological high-quality development, and in the future, we should pay attention to desertification prevention and control and promote forest and grassland construction, so as to provide a guarantee for improving the regional ecological security pattern and sink enhancement policies.