Farmland non-point source pollution has become one of the main causes of water eutrophication. In order to reduce nitrogen loss and relieve the over loading of nutrients in the local water body of rice field, a pot experiment was carried out. The main plots were continuous flooding irrigation (I_F) and alternate wet and dry irrigation (I_A), and the subplots were a control (conventional nitrogen application, N1C0) and four different nitrogen and nitrogen-loaded biochar treatments (N3/4C1,N3/4C2, N1/2C1, N1/2C2), in which N3/4 and N1/2 represented that the nitrogen application amount was 3/4 times and 1/2 times of the local traditional nitrogen application amount (N1); C1 and C2 were respectively 10 t/hm² and 20 t/hm² nitrogen-loaded biochar. Results showed that: (1) The pH value of the surface water with the conventional nitrogen treatment was significantly increased by reducing the application of nitrogen fertilizer and nitrogen-loaded biochar; (2) The average concentration of NH₄⁺—N in the surface water of I_A was 8.0% higher than that of I_F, but the average concentration of NH₄⁺—N in the surface water of I_A was lower than that of I_F after adding 20 t/hm² nitrogen-loaded biochar; (3) In the later growth stage of rice, the nitrogen-loaded biochar had a significant slow-release effect on NH₄⁺—N, while in I_A, the reduction of nitrogen fertilizer combined with nitrogen-loaded biochar reduced the concentration of NO₃^-—N in the surface water compared with the treatment of N1C0. (4) The tillering rate of rice could be increased by reducing nitrogen application and adding nitrogen-loaded biochar, while the effective tillering rate of rice could be improved by adding 20 t/hm² nitrogen-loaded biochar when the amount of nitrogen application was less. In summary, reducing nitrogen application combined with adding nitrogen-loaded biochar could not only reduce the nitrogen content by about 30.8% in eutrophic water, but also significantly reduced the NH₄⁺—N concentration in surface water at the early stage of fertilization, reduced the risk of loss, prolonged the release time of NH₄⁺—N, reduced the nitrogen application amount by 25% and ensured the nitrogen demand at the end of rice growth, which was conducive to rice growth.