To investigate the effect of organic fertilizer nitrogen replacing chemical fertilizer nitrogen on cotton yield and soil fertility in saline alkali soil，the effects of no fertilizer(CK)，farmers’ conventional fertilizer and different organic fertilizer nitrogen replacing rate of 15%，30% and 45% of chemical fertilizer nitrogen on cotton yield and soil fertility were examined by field experiments under the condition of flood irrigation in Awati county，south Xinjiang.The results showed that the effect of replacing 15% of chemical fertilizer nitrogen with organic fertilizer nitrogen was obvious，especially under the condition of straw returning and soil amendments，the yield of replacing 15% of chemical fertilizer nitrogen with organic fertilizer nitrogen was 15.18% higher than that of chemical fertilizer alone.Under the condition of straw returning to the field，the contents of soil available P and K were significantly higher in the treatment of organic fertilizer nitrogen replacing 45% of chemical fertilizer nitrogen than other treatments； under the condition of adding soil amendments，the contents of soil organic matter and alkali hydrolyzed N were significantly higher than other treatments.In the treatment of different organic fertilizer nitrogen instead of chemical fertilizer nitrogen，the soil salt content was lower than that of CK treatment，and decreased with the increase of soil profile depth.The results reflected that organic fertilizer substitution of chemical fertilizer have beneficial effects on maintaining cotton yield.