Accounting for one quarter of China’s land area, the endorheic Shiyang River basin is a vast semi-arid to arid region in China’s northwest. Exploring the impact of changes in land use on this arid area’s carbon budget under global warming is a key component to global climate change research. Variation in the region’s soil carbon storage due to land use changes occurring between 1973 and 2012 was estimated. The results show that land use change has a significant impact on the soil carbon budget, with soil carbon storage having decreased by 3.89 Tg between 1973 and 2012. Grassland stored the greatest amount of soil carbon (114.34 Mg ha−1), whereas considerably lower carbon storage occurred in woodland (58.53 Mg ha−1), cropland (26.75 Mg ha−1) and unused land (13.47 Mg ha−1). Grasslands transformed into cropland, and woodlands degraded into grassland have substantially reduced soil carbon storage, suggesting that measures should be adopted to reverse this trend to improve soil productivity.