Greenhouse gas cause the global warming has become a big problem in the world. Farmland ecosystem play an important role in carbon cycle and carbon balance. In this research we used the Open Eddy Covariance to do an insitu observation,and did some research about NEE(Net Ecosystem Exchange),analyzed the relationship between carbon source and sink of farmland ecosystem. The results showed that in cotton field ecosystem the NEE variations were the U - shape curve in budding stage,flowering stage and bolling stage; the biggest NEE appeared at 3: 00 AM,4: 00AM and 1: 00AM for budding stage,flowering stage and bolling stage,and there were 9.45umol?m~(-2)?s~(-1),8.78umol?m~(-2)?s~(-1),and 7.68umol?m~(-2)?s~(-1); the lowest NEE appeared at 14: 00 PM,15: 00PM and 15: 00PM,there were - 19.35umol?m~(-2)?s~(-1),- 21.73umol?m~(-2)?s~(-1) and - 20.51umol?m~(-2)?s~(-1). The NEE value was negative at night,it showed the cotton fields ecosystem was in the carbon emissions; during the day NEE value was positive,it showed that the cotton fields ecosystem was in the carbon absorption. NEE variation was a " U" type curve for a month,but the change was not big. The three growing stages were all for the carbon storage; the carbon storage in flowering stage was the largest(- 7.26g? m~(-2)?s~(-1)),next was in budding stage (- 6.31g?m~(-2)?s~(-1)),and the bolling stage (- 5.37g?m~(-2)?s~(-1)). Temperature and rainfall had an obvious effect for carbon storage. In arid area's agricultural ecosystem the carbon storage was obviously a process of carbon sink.