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Understanding the influence of farming practices on carbon (C) cycling is important for maintaining soil quality and mitigating climate change, especially in arid regions where soil infertility, water deficiency, and climate change had significantly influenced on agroecosystem. A field experiment was set up in 2009 to examine the influence of residue management and fertilizer application on the C cycle in a cotton field in the Xinjiang Uygur Autonomous Region of Northwest China. The study included two residue management practices (residue incorporation (S) and residue removal (NS)) and four fertilizer treatments (no fertilizer (CK), organic manure (OM), chemical fertilizer (NPK), chemical fertilizer plus organic manure (NPK+OM)). Soil organic carbon (SOC) and some of its labile fractions, soil CO2 flux, and canopy apparent photosynthesis were measured during the cotton growing seasons in 2015 and 2016. The results showed that SOC, labile SOC fractions, canopy apparent photosynthesis, and soil CO2 emission were significantly greater in S+NPK+OM (residue incorporation+chemical fertilizer) than in the other treatments. Analysis of all data showed that canopy apparent photosynthesis and soil CO2 emission increased as SOC increased. The S+OM (residue incorporation+organic manure) and S+NPK+OM treatments were greater for soil C sequestration, whereas the other treatments resulted in soil C loss. The S+ NPK treatment is currently the standard management practice in Xinjiang. The results of this study indicate that S+ NPK cannot offset soil C losses due to organic matter decomposition and autotrophic respiration. Residue return combined with NPK fertilizer and organic manure application is the preferred strategy in arid regions for increasing soil C sequestration.