An experiment was carried out in two soils of oasis farmland and the surrounding desert at the southern periphery of the Gurbantonggut Desert, in central Asia, to test the effects of land use on soil organic carbon (SOC) stock and carbon efflux in deep soil. The result showed that although SOC content in the topsoil (0-0.2 m) decreased by 27% after desert soil was cultivated, total carbon stock within the soil profile (0-2.5 m) increased by 57% due to the significant increase in carbon stock at 0.2-to 2.5-m depth, and carbon efflux also markedly increased at 0-to 0.6-m depth. In the topsoil, the carbon process of the oasis was mainly dominated by consumption; in the subsoil (0.2-0.6 m) it was likely to be co-dominated by storage and consumption, and the greatest difference in SOC stock between the two soils also lay in this layer; while in the deep layer (0.6-2.5 m) of the oasis, with a more stable carbon stock, there was carbon storage dominated. Moreover, carbon stocks in the deep layer of the two soils contributed about 65% of the total carbon stocks, and correspondingly, microbial activities contributed 71% to the total microbial activity in the entire soil profile, confirming the importance of carbon cycling in the deep layer. Desert cultivation in this area may produce unexpectedly high carbon stocks from the whole profile despite carbon loss in the topsoil.