Abstract: Agricultural non-point source pollution in Hetao Irrigation Area of Inner Mongolia has been the main source of pollution in the Yellow River. There was the need to reduce the use of fertilizer in the croplands of the Yellow River Basin. This study explored the application effects of nitrogen (N) and phosphorus (P) fertilizers of wheat-maize intercropping, the conventional cropping systems in the Hetao Irrigation Area of Inner Mongolia. The results showed that under wheat and maize intercropping, the relationship between yield and nitrogen/phosphorus fertilization rate was best explained by quadratic regression model. Nitrogen, phosphorus and nitrogen plus phosphorus interactions had a significant effect on wheat-maize yield. The order of significance of the effect was N+P > N > P. With low fertilization, the synergistic enhancement effect of nitrogen and phosphorus fertilizers on yield was high. Beyond the threshold value, nitrogen and phosphorus fertilizer antagonistic limited wheat-maize yield. N₂P₂ (180 kg·hm^-2 N and 157.50 kg·hm^-2 P₂O₅ for wheat, 270 kg·hm^-2 N and 180 kg·hm^-2 P₂O₅ for maize) treatment satisfied the demands for crop growth and development in wheat-maize intercropping and there was fully efficacy in fertilizer use. With further increase in fertilizer, however, nitrogen uptake by crops increasingly limited fertilizer use efficiency and fertilizer utilization by crops continuously declined. Based on the of single- and double-factor effect analysis of nitrogen and phosphorus fertilizer, the best nitrogen application rate for wheat was 167.67 196.61 kg·hm^-2 and the best phosphorus application rate for wheat was 130.43 186.64 kg·hm^-2. Also the best nitrogen application for maize was 222.10 299.14 kg·hm^-2 and the best phosphorus application for maize was 156.14 188.00 kg·hm^-2. This finding was useful for reducing the application of nitrogen and phosphorus fertilizers and improving soil nutrient balance in the Yellow River Basin. It also provided a useful guidance on the mode of reducing agricultural non-point source pollution in the Yellow River Basin.