Soil organic carbon (SOC) constitutes a large pool within the global carbon cycle. Changes in land-use/cover strongly drive variation of SOC stocks. We analyzed the changes in four types of land use/cover and their influence on SOC content, density, and regional stocks along the main channel of the Tarim River in China for 2000-2010 obtained from remotely sensed images and field surveys. The areas and structures of the land uses/covers changed greatly during this period. Specifically, the areas of cultivated, industrial and residential, and shrub land increased, particularly cultivated and shrub land. The areas of forestland, grassland, water bodies, and unused land decreased. SOC stocks in forestland, grassland and unused land decreased between 2000 and 2010. The total SOC stock for the forestland shrub land grassland and unused land was lower in 2010 than 2000. Land-use/cover conversion thus affected SOC stocks. Specifically, conversions from forestland to shrub land, forestland to grassland, forestland to unused land, grassland to shrub land, grassland to unused land, and shrub land to unused land decreased the SOC stocks. This study provides a scientific basis for eco-environmental protection in arid areas.