To relieve the situation of the agricultural nonpoint pollution (NPS) in south and east China, paddy field controlled drainage (PFCD) is applied as an important and efficient approach to agricultural water management. A series of PFCD tests at four major growth stages of rice were conducted by use of 18 lysimeters. Concentration of ammonia nitrogen (NH4+-N) and nitrate nitrogen (NO3--N) in surface and subsurface paddy water was observed. The results indicated that the concentration of NH4+-N and NO3--N in paddy water declined with the persistence of a waterlogged condition. Compared to traditional drainage, PFCD reduced N loss in surface water by 95.6%, 78.7%, 59.6%, and 87.4% at the stage of tillering, jointing-booting, heading-flowering, and milking, respectively. It should be noted that loads of N losses in surface water increased on the fourth day after waterlogging at the jointing-booting and milking stage, and surface water exhibited higher N concentration on the first day after waterlogging at each stage. Therefore, paddy field surface water drainage should be avoided in these periods.