The changes of the concentration of nitrogen and phosphorus in the multiple cropping system of rapeseed-rice， the cumulative loss of nitrogen and phosphorus in the runoff water and the yield of crops were studied through the positioning monitoring test under three different modes of fertilization including the optimization of principal factor， the integrated optimization and the conventional treatment to investigate the effects of optimized fertilization on the yield of crops and the dynamic changes of the loss of nitrogen and phosphorus in the runoff water of paddy field.The results showed that the content of total nitrogen， nitrate nitrogen， total phosphorus and soluble phosphorus in the runoff water during the whole growth period increased first， then decreased， and then tended to be stable， while the content of ammonium nitrogen in rapeseed was always low.Compared with the conventional treatment， the average content of total nitrogen， ammonium nitrogen and nitrate nitrogen in the runoff water under the principal factor optimization decreased by 31.44%， 45.45% and 28.84%， respectively.The accumulative loss of total nitrogen， ammonium nitrogen and nitrate nitrogen under conventional treatment were 10.92 kg/hm²， 0.37 kg/hm² and 9.16 kg/hm²， respectively.Under the principal factor optimization and the integrated optimization， the cumulative loss of the total nitrogen， ammonium nitrogen and nitrate nitrogen decreased by 31.41% and 22.99%， 2.71% and 43.24%， 31.01% and 29.81%， respectively.The yield of rapeseedseed under the integrated optimization was 1 954.6 kg/hm²， which was 4.60% and 4.79% higher than that under the principal factor optimization and conventional treatment， respectively.The yield of rice under integrated optimization was 6 375.5 kg/hm²， which was 3.76% and 0.81% higher than that under the principal factor optimization and conventional treatment， respectively.It is indicated that the integrated optimization can not only significantly improve the yield of crops， but also effectively reduce the risk of the loss of nitrogen and phosphorus in paddy fields compared with conventional fertilization， which is of great significance for protecting the environment and controlling the pollution of non-point source.