Abstract: Application of organic fertilizer could improve soil moisture, promote water use efficiency and increase crop yield. We conducted an experiment to study the effects of soil water storage, photosynthetic indexes and water use efficiency under different application rate of organic fertilizer (H: 90000 kg/ha, M: 60000 kg/ha, L: 30000 kg/ha) for four years (20072010) in semi-arid areas of southern Ningxia. The results showed that compared with CK, after 4 years continuous application of organic fertilizer, following the order of organic fertilizer rate from high to low, soil water storage (depth 0200 cm) increased by 6.46%, 5.06% and 2.12% at the sowing stage and by 12.47%, 9.38% and3.58% at the maturity stage of winter wheat respectively; grain yield of winter wheat increased by 35.05%, 20.77% and 11.51% (P0.01) respectively; and the water use efficiency increased 38.26%, 22.61% and 11.88% (P0.01) respectively. Application of organic fertilizers not only could significantly increase SPAD value, but also enhance Photosynthetic efficiency. The net photosynthetic rate and transpiration rate for the H,M and L treatments are about 5.79,4.68,2.00 mol /(m2?s) and 1.50,1.17,0.57 mmol/(m2?s)higher than that of the CK(P0.01). In conclusion, in semi-arid areas of southern Ningxia, the application of organic fertilizer could enhance soil moisture content, promote photosynthetic efficiency, increase crop yield and crop water use efficiency significantly.