Abstract: The regulating effects of irrigation and nitrogen fertilizer application on net photosynthetic rate in flowering and boll-forming stages and yield in cotton were studied on a sandy farmland in the marginal oasis in the middle of Heihe River basin. Two elements including 3 irrigation levels and 5 nitrogen fertilizer levels were set up. The results showed that both average daily net photosynthetic and transpiration rates of cotton leaves in flowering and boll-forming stages increased with nitrogen fertilizer application rates, but slightly declined when nitrogen fertilizer application exceeded 300 kg/ha. Compared with zero nitrogen fertilizer application, seed cotton yield were 33.9%, 45.8%, 50.9% and 49.2% higher and irrigation water productivity were 33.3%、45.8%、50% and 50% higher under nitrogen fertilizer application of 150, 225, 300 and 375 kg/ha, respectively. There was no significant difference on seed cotton yield between 3 irrigation levels. Irrigation water productivity（IWP）was decreased with the increase of irrigation levels. Significant positive correlations were found between net photosynthetic rates in flowering and boll-forming stages and seed cotton yield, straw biomass, boll number on individual plant, boll weight, and seed weight. These results suggested that irrigation and nitrogen fertilizer applications had a significant influence on net photosyntheticrate of cotton leaves in flowering and boll-forming stages, and on the growth of cotton and seed cotton yield. There was higher photosynthetic efficiency. The maximum seed cotton yield and irrigation water productivitywas observed under nitrogen fertilizer applications of 300 kg/ha in the marginal oasis in the middle of Heihe River basin. Reduction irrigation rate from 10800 m3/ha to 8100 m3/ha had no effect on cotton yield.