Rice-wheat rotation is a typical intensive cropping system for food production with application of huge amounts of chemical fertilizers in the Tai Lake Basin and the control of nitrogen and phosphorus runoff losses is widely concerned. In this paper, the effects of two different fertilization modes including farmer practice (FP) and optimized control fertilization (CM)on crop yield and partial productivity of nitrogen and phosphorus fertilizers were investigated with a large-area field comparison experiment. Meanwhile, the characteristics of nitrogen and phosphorus forms in runoff water and the differences of nitrogen and phosphorus runoff losses were explored.The results showed that rice or wheat above-ground total biomass, grain yield, nutrient (nitrogen, phosphorus and potassium) contents and accumulation in plant ground parts of CM mode were not significantly (P>0.05) different from those of FP mode. The rice or wheat grain partial productivity of nitrogen fertilizer of CM mode was significantly (P<0.05) greater than that of FP mode, the same results was found for phosphate fertilizer. The concentrations of all nitrogen and phosphorus forms in runoff water of CM mode during rice and wheat growth seasons were lower than those of FP mode, even significantly (P<0.05). In the rice or wheat growth season and the whole rotation period, the cumulative losses of total nitrogen or total phosphorus of CM mode were significantly (P<0.05) less than that of FP mode. Optimized control fertilization mode could not only maintain the grain yield of rice and wheat, but also significantly reduce the runoff losses of nitrogen and phosphorus in the rice-wheat rotation system, which could be promoted and utilized in actual agricultural production.