Clarifying the synergistic effect between rainfall and fertilization in rainfed farming and joint effect on crop yield can provide theoretical basis for improving the sustainable productivity of farmland in dry farming. A 32-year fertilizer regulation experiment was conducted in the dry farming region of the Loess Plateau. According to the precipitation, it was divided into dry, normal and high rainfall years. The influence of long-term fertilization regulation on crop yield and farmland moisture changes under different rainfall years was analyzed, and the regulation mechanism of fertilization and precipitation coordination on crop yield under different rainfall years was explored. The results showed that effects of fertilization on crop yield and water use efficiency (WUE) were closely related to experimental years. In the early stage, the increase in treatments with higher amounts of nitrogen was more significant, while in the later stage, the increase in treatments with less organic fertilizer was more significant. The correlation of crop yield, the whole rainfall (WR), growth period rainfall (GPR), fallow period rainfall (FPR), water storage during sowing (SWS), evapotranspiration (ET), WUE and utilization efficiency of precipitation (PUE)under different rainfall years and treatments was analyzed. The results showed that the crop yield showed that the correlation with PUE showed high> dry> normal rainfall year, and the correlation with WUE showed the law of dry> high> normal rainfall year. The correlation of organic fertilizer treatments was lower than that of single chemical fertilizer. With the years extension of application organic fertilizer, application low amount of organic fertilizer can improve crop yield by improving PUE, and can achieve the effect of application high amount of organic fertilizer. No matter what the rainfall years, the long-term application of organic fertilizer can make full use of the rainfall to improve the WUE, and then ensure the sustainability of crop yield.