Abstract: Abstract: Attempts to reduce the nutrient losses in drainage water have led to the promotion of controlled irrigation and drainage. Under the controlled irrigation and drainage condition, alternate drought and flooding condition (drought then flooding (HZL) and flooding then drought (LZH)) often occur. It is unclear about the change of nitrogen and phosphorus concentration in paddy water affected by controlled irrigation and drainage under the alternate stress. Therefore, this study based on farmland water depth as the control index aimed to investigate dynamic changes of nitrogen and phosphorus concentration in underground water and surface water of paddy field under the controlled irrigation and drainage in the HZL and LZH condition. Moreover, the effect of controlled irrigation and drainage on the discharge-reducing and water saving was studied. The experiments were conducted in specially designed experimental pits in Jiangning Water-saving Experiment Station at the Key Laboratory of Efficient Irrigation-Drainage and Agricultural Soil-Water Environment in Southern China, Ministry of Education, Nanjing (31?86?N, 118?60?E) during the rice growing season of 2015 (May to October). Eight controlled irrigation and drainage treatments were designed for the experiment. For the HZL treatments, rice experienced the drought stress at first, and when the field water depth dropped to the lower limit (?500 mm) the irrigation water was added with an auto-irrigation system until the upper limit of water depth (200 mm at the tillering stage and 250 mm at the other stages) was reached. For the LZH treatments, rice experienced the flooding stress at first, and then irrigation water was immediately added to the upper limit of water depth (200 mm at tillering stage and 250 mm at the other stages); the field surface water was then drained and the field water depth dropped to the lower limit (?500 mm). The controlled irrigation was considered as the control with irrigation lower limit of -200 mm and the upper limit of 20 mm for the tillering stage and 50 mm for the other stages. Ammonia N (NH4+-N), nitrate N (NO3?-N), and total phosphorus (TP) in the water samples were analyzed. The results showed that when the HZL treatments had higher NH4+-N, NO3?-N and TP concentration during the earlier period of flooding, therefore, the surface and underground drainage should be noticed. Extending the flooding days could decrease nitrogen and phosphorus concentration in the controlled irrigation and drainage. The NH4+-N was the major form of N in the surface drainage and percolation water. The TP concentration in the surface water followed a decreasing trend during the flooding. Compared to the controlled irrigation, under the controlled irrigation and drainage, the irrigation amount was reduced by 7.4%-18.5%, the drainage amount was reduced by 23.0%-43.5%, the NH4+-N load was reduced by 18.5%-54.5%, the NO3?-N load was reduced by 16.8%-57.7% and the TP load was reduced by 34.2%-58.3%. Meanwhile, most of the controlled irrigation and drainage treatments could keep high rice grain yield. In sum, the controlled irrigation and drainage could achieve a positive effect on grain yield, water saving and N-P loss reduction at the jointing-booting stage and heading and flowering stage. Therefore, the controlled irrigation and drainage technology has a good effect on water saving and N and P loss reduction and provides a guide for the irrigation and drainage.