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Monitoring soil CO2 respiration with chamber measurements and identifying controlling factors such as the diversity of vegetation species, moisture and temperature can help guide desert scrubland management. Soil CO2 respiration and potential controlling factors at four sites in desert scrubland were examined along the Sangong River Basin (SRB) in northwestern China in 2004. Soil CO2 respiration descended along the SRB as did the diversity of vegetation species, air temperature and air humidity. The two sites of the field station (FS) and the north desert (ND) and the low reaches of the SRB among these locations were monitored to analyze the effects of pH value, soil organic carbon (SOC), total nitrogen (TN) and calcium carbonate (CaCO3) on soil CO2 respiration during the growing season in 2005. The ND site was located at the southern edge of the Gurbantunggut Desert; the FS site was in the border area of the SRB Alluvial Fan. One-way ANOVA was performed. The result showed that air humidity and CaCO3 content had a strong influence on soil CO2 respiration; SOC content was a limitation to soil CO2 respiration in the arid-desert zone. Effective management activities can attenuate soil CO2 respiration and keep carbon balance trends at a desirabe level in desert scrublands.