[Objective] The changes of nitrogen and phosphorus and algae in the water under "rice-duck-shrimp ecological planting and breeding model were studied in order to provide a scientific reference for controlling agricultural non-point source pollution caused by nitrogen and phosphorus in the drainage of rice fields and improving the ecological environment of rice fields.[Methods] The differences and advantages of different planting modes were analyzed by comparing the ecological planting and breeding model of rice-duck-shrimp and the conventional planting model. The study focused on the impact of the internal synergy of rice-duck-shrimp on the changes of nitrogen, phosphorus and algae in water.[Results] ① The contents of total nitrogen(TN) and total phosphorus(TP) in rice-duck-shrimp ecological paddy field reduced by 32.43% and 19.35%, respectively. The removal rates of total TN and total TP in initial irrigation water were 38.7% and 26.9%, respectively. ② The changes of nitrogen and phosphorus forms were altered by the ecological planting and breeding mode of rice-duck-shrimp. During the whole growth period of rice, the proportion of soluble phosphorus(DTP) and granular phosphorus(PP) was more stable. However, the proportion of organic nitrogen(ON) in paddy water significantly increased in the later period of rice. ③ The rice-duck-shrimp ecological planting breeding model could improve the community structure of algae in water. The algae biodiversity index in paddy field drainage increased to 2.34. ④ Compared with conventional cultivation, the effective panicles, grains per spikee and seed setting rate of rice in rice-duck-shrimp ecological planting breeding model increased by 4.83%, 5.28% and 2.84%, respectively. Moreover, the protein content of rice increased by 8.15%, which significantly improved the economic benefits.[Conclusion] Compared with conventional cultivation, rice-duck-shrimp ecological planting and breeding model could not only effectively reduce the content of N and P in rice field water, increase the stability of water, but also improve the effective panicles, grains per spike and seed setting rate of rice, which increases economic benefits and does not bring the risk of heavy metal pollution. Therefore, it was worth popularizing as a farming technology.