Xinjiang is one of the three major cotton-producing areas in China, and provided 45% of the nations production. Due to the intensive agricultural management, the cotton planting in Xinjiang go through three cropping periods in 1980—2013. The three cropping periods are as following: period of furrow irrigation with non-mulching (NF period, 1980—1993), period of furrow irrigation with mulching (MF period, 1994—2004) and period of drip irrigation with mulching (MD period, 2005—2013). Under the condition of sufficient irrigation, the seed yield of cotton was closely influenced by air temperature, and the evapotranspiration was more related to irrigation water amount. The seed yield reached the maximum value of 4493.3 kg/hm2 in MD period, while ET had the peak value of 714 mm in NF period. In the recent 34 years, the seed yield and evapotranspiration of cotton were generally increased. The annual increasing rate of seed yield (83.97 kg/hm2) was greater than that of evapotranspiration (5.46 mm). Thus water use efficiency (WUE) and irrigation water use efficiency (IWUE) of cotton were also increased. WUE and IWUE reached the peak value of (0.7±0.1) kg/m3 and (1.0±0.3) kg/m3, respectively, which were close to the levels in humid regions.