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Carbon neutrality is an important target in China's efforts to combat the climate crisis. The implementation of carbon neutrality requires high crop yields in farmland ecosystems of arid regions. However, the responses of farmland ecosystems to environmental changes and their effects on the conversion and intensity of carbon sources/sinks within farmlands in arid regions remain unclear, which limits carbon sequestration. In this study, we used a set of eddy covariance systems to observe carbon and water fluxes in cotton and spring maize, two typical crops in arid regions of Northern Xinjiang in China. The carbon and water exchange and water use efficiency (WUE) of cotton and spring maize were evaluated over the entire growth cycle with respect to changes in the environment. Our results show that the carbon sequestration capacity of farmland ecosystems in arid regions is undeniable and is strongly influenced by the growth and development of plants. Spring maize, as a representative of C4 plants, exhibited a 58.4% higher carbon sequestration efficiency than cotton, a C3 plant, and they both reached their carbon sequestration efficiency peak in July. Throughout the growth period, temperature, net surface radiation, and saturated vapor pressure differences (VPD) significantly affected the carbon sequestration capacity and WUE of both crops. Optimal temperatures can maximize the carbon sequestration efficiency of cotton and spring maize; for cotton, they are 20–25 °C, and for spring maize, they are 22–27 °C, respectively. In addition, it is recommended that spring maize be harvested at the end of July when it meets the harvesting standards for silage feed and achieves the maximum carbon sequestration. Afterward, winter crops should be planted to maximize the yield and improve the carbon sequestration capacity of farmlands. [ABSTRACT FROM AUTHOR]