Carbon and water fluxes of cotton field with plastic mulched drip irrigation were measured using an eddy covariance (EC) technique in 2009, 2010, 2012 and 2013 at Wulanwusu experimental station, which was a representatively agricultural oasis in northern Xinjiang. The diurnal pattern of mean monthly gross primary production (GPP) and net ecosystem exchange (NEE) showed an obviously sinusoidal dynamic from June to September, whilst that of ecosystem respiration (Res) stayed low and stable between daytime and nighttime. The response of daytime hourly GPP to net solar radiation (Rnet) could be expressed by a rectangular hyperbolic function. The variations of maximal assimilation rate (A) were followed changes in LAI, and the peak value occurred in July. The seasonal variations of GPP and NEE were close to the cotton phenology, and they almost reached the peak value in July. However, seasonal variations of Res didn’t follow that of LAI, and the maximum value occurred nearly one month earlier than that of LAI. Seasonal NEE showed a carbon sink from squaring to harvest period, whilst it indicated a carbon source before the squaring time as well as after the harvest time. The cumulative GPP averaged 816.2gC/m2 during the growing season (from April to October), and more than half of GPP was partitioned into NEE (meanly -478.6gC/m2).