The field experiments with different volume of irrigation water and application modes of nitrogen fertilizer including N0：0 kg/hm²， N240：240 kg/hm²， N360：360 kg/hm²， W1：3 600 m³/hm²， W2：4 200 m³/hm²， and W3：5 400 m³/hm² were conducted in cotton at the stage of flowering and bolling in Alar region， Xinjiang to study the effects of different water nitrogen ratio on the spatial and temporal distribution of soil inorganic nitrogen and the yield of cotton. The contents of nitrate nitrogen and ammonium nitrogen in soil layers of 0-30 cm and 30-60 cm， and the yield of cotton were measured. The optimal fertilization volume and irrigation input of cotton planting period were obtained through comprehensive comparative analysis. The results showed that nitrogen application of N240 and N360 significantly increased the content of nitrate nitrogen in cotton root layer at stage of flowering and bolling. Under fertilization treatment，The content of soil ammonium nitrogen had a short-term upward trend with the increase of irrigation level， and then reduced to the level before irrigation. Under the conditions of W2 irrigation volume and N240 nitrogen application volume， the yield of cotton reached 6 648.05 kg/hm² by applying 42% of the total fertilizer volume and 57% of the total irrigation volume in cotton at the stage of flowering and bolling. It is indicated that the yield of cotton is the highest under the conditions of W2 irrigation volume and N240 nitrogen application volume， which is the optimal volume of fertilization and irrigation for cotton at the stage of flowering and bolling in Alar region of Xinjiang.