Soil organic carbon (SOC) storage generally represents the long-term net balance of photosynthesis and total respiration in terrestrial ecosystems. However, soil erosion can affect SOC content by direct removal of soil and reduction of the surface soil depth; it also affects plant growth and soil biological activity, soil air CO2 concentration, water regimes, soil temperature, soil respiration, carbon flux to the atmosphere, and carbon deposition in soil. In arid and semi-arid region of northern China, wind erosion caused soil degradation and desert expansion. This paper estimated the SOC loss of the surface horizon at eroded regions based on soil property and wind erosion intensity data. The SOC loss in China because of wind erosion was about 75 Tg C yr−1 in 1990s. The spatial pattern of SOC loss indicates that SOC loss of the surface horizon increases significantly with the increase of soil wind erosion intensity. The comparison of SOC loss and annual net primary productivity (NPP) of terrestrial ecosystem was discussed in wind erosion regions of China. We found that NPP is also low in the eroded regions and heavy SOC loss often occurs in regions where NPP is very small. However, there is potential to improve our study to resolve uncertainty on the soil organic matter oxidation and soil deposition processes in eroded and deposited sites.