[Objective] The influence of land use change patterns on the spatial distribution of carbon sinks for the Inner Mongolia section of the Yellow River basin was investigated, and the main driving factors behind the spatial distribution of carbon sinks were identified in order to provide a basis for directing ecological spatial development and for developing sink enhancement policies in the study area.[Methods] The study was conducted for the Inner Mongolia section of the Yellow River basin. InVEST-FLUS model was used to analyze changes in the carbon sink capacity during each period of the study based on land use data from 2000, 2010, and 2020. The patterns of carbon stock changes were simulated in 2040 under three different scenarios (natural development, ecological conservation and agricultural priority), and identified the main driving factors behind the differences in the spatial distribution of carbon sinks with the help of geographic probes.[Results] ① From 2000 to 2020, carbon storage for the Mongolia section of the Yellow River basin initially increased and then decreased, with an overall increase of 8.63×10⁶ t. Subsurface biological carbon storage increased by 3.91×10⁶ t and soil carbon storage increased by 2.28×10⁶ t. ② Carbon storage continued to decrease by 3.92×10⁶ t for the future natural development scenario, but increased by 2.21×10⁷ t for the ecological protection scenario, which was higher than for the agricultural priority scenario (4.99×10⁶ t). Soil carbon storage was the key factor causing the incremental difference. ③ The unbalanced distributions of mean annual rainfall and mean annual temperature were the main factors causing differences in the various carbon pools for the Mongolia 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. Future attention should be given to preventing and controlling desertification, and to promoting forest and grassland construction so as to improve the regional ecological security pattern and carbon sink enhancement policies.