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Changes in both soil organic C storage and soil respiration in farmland ecosystems may affect atmospheric CO2 concentration and global C cycle. The objective of this field experiment was to study the effects of three crop field management practices on soil CO2 emission and C balance in a cotton field in an arid region of Northwest China. The three management practices were irrigation methods (drip and flood), stubble managements (stubble- incorporated and stubble-removed) and fertilizer amendments (no fertilizer (CK), chicken manure (OM), inorganic N, P and K fertilizer (NPK), and inorganic fertilizer plus chicken manure (NPK+OM)). The results showed that within the C pool range, soil CO2 emission during the whole growing season was higher in the drip irrigation treatment than in the corresponding flood irrigation treatment, while soil organic C concentration was larger in the flood irrigation treatment than in the corresponding drip irrigation treatment. Furthermore, soil CO2 emission and organic C concentration were all higher in the stubble-incorporated treatment than in the corresponding stubble-removed treatment, and larger in the NPK+OM treatment than in the other three fertilizer amendments within the C pool range. The combination of flood irrigation, stubble incorporation and application of either NPK+OM or OM increased soil organic C concentration in the 0-60 cm soil depth. Calculation of net ecosystem productivity (NEP) under different management practices indicated that the combination of drip irrigation, stubble incorporation and NPK+OM increased the size of the C pool most, followed by the combination of drip irrigation, stubble incorporation and NPK. In conclusion, management practices have significant impacts on soil CO2 emission, organic C concentration and C balance in cotton fields. Consequently, appropriate management practices, such as the combination of drip irrigation, stubble incorporation, and either NPK+OM or NPK could increase soil C storage in cotton fields of Northwest China.