To mitigate impacts of sandstorms on northern China, the Chinese government launched the Beijing–Tianjin Sand Source Control Program (BTSSCP) in 2000. The associated practices (i.e., cultivation, enclosure, and aerial seeding) were expected to greatly enhance grassland carbon sequestration. However, the BTSSCP-induced soil organic carbon (SOC) dynamics remain elusive at a regional level. Using the Xilingol League in Inner Mongolia for a case study, we examined the impacts from 2000 to 2006 of the BTSSCP on SOC stocks using the IPCC carbon budget inventory method. Results indicated that over all practices SOC storage increased by 1.7%, but there were large differences between practices. SOC increased most rapidly at the rate of 0.3 Mg C·ha–1·yr–1 under cultivation, but decreased significantly under aerial seeding with moderate or heavy grazing (0.3 vs.0.6 Mg C·ha–1·yr–1). SOC increases varied slightly for grassland types, ranging from 0.10 Mg C·ha–1·yr–1 for temperate desert steppe to 0.16 Mg C·ha–1·yr–1 for temperate meadow steppe and lowland meadow. The overall economic benefits of the SOC sink were estimated to be 4.0 million CNY. Aerial seeding with no grazing was found to be the most cost-effective practice. Finally, we indicated that at least 55.5 years (shortest for cultivation) were needed for the grasslands to reach their potential carbon stocks. Our findings highlight the importance and effectiveness of BTSSCP in promoting terrestrial carbon sequestration which may help mitigate climate change, and further stress the need for more attention to the effectiveness of specific practices.