Abstract: To solve the uncertain problem of calculation of nitrogen and phosphorus loss in the soils, considering the difference of combination type between nitrate, ammonium and soil particle, quantitative evaluation method of nitrogen losses based on nitrogen cycle was established for calculating the Yongding River Basin soil nitrogen and phosphorus loss. Combined with the characteristics of closely relationship between the movement of phosphorus and soil styles, phosphorus loss based on farmland runoff was determined by computing the content of dissolved phosphorus and particulate phosphorus. Amount of nitrogen and phosphorus loss in Yongding River Basin were 96 kg/hm2 and 9 kg/hm2, respectively; the differences of which among the basin was significant. The soil and characteristics of chemical fertilization application were considered in the method of calculation of nitrogen and phosphrus loss amout, so the results of calculation was reasonable and suitable for the study area. The study provides a reference for calculation of nitrogen and phosphrus loss and agricultural point source pollution control.