In the field plot experiment of the Chaohu Paihe small watershed, four treatments, including T1 (conventional compound fertilizer), T2 (bio-organic fertilizer replacing 30% nitrogen fertilizer), T3(loss-of-control fertilizer replacing 30% nitrogen fertilizer), and T4 (bio-organic fertilizer and loss-of-control fertilizer replacing 15% nitrogen fertilizer respectively) were set up to study the effects of dynamic changes of nitrogen and phosphorus concentrations in the surface water, nitrogen and phosphorus loss in the runoff, and rice yield under several different fertilization modes. The results showed that the average concentrations of total nitrogen and total phosphorus in the surface water of treatment T1 were 10.30 and 0.45 mg/L, respectively. Compared with treatment T1, the average concentrations of total nitrogen in the surface water of treatment T2, T3, and T4 decreased by 12.2%, 6.5%, 5.3%, the average concentrations of total phosphorus in the surface water decreased by 26.7%, 15.6% and 13.3%, respectively.The total loss of total nitrogen and total phosphorus in the runoff with treatment T1 reached 17.68 and 1.60 kg/hm². Compared with treatment T1, the total loss of total nitrogen in the runoff of treatment T2, T3, and T4 decreased by 35.0%, 30.8% and 25.5%, the total loss of total phosphorus in the runoff of treatment T2, T3, and T4 decreased by 16.3%, 21.9% and 22.5%, respectively. The yield of grain of treatment T1 was 8.95 t/hm². The yields of treatment T2 and T4 increased by 7.8% and 6.5%, respectively, showing a significant difference with T1. The yield of treatment T3 decreased by 2.2% compared with T1, and the difference was not significant. The experimental results show that compared with treatment T1(conventional compound fertilizer), T2(bio-organic fertilizer replaces 30% nitrogen fertilizer), and T4(bio-organic fertilizer and loss-of-control fertilizer replacing 15% nitrogen fertilizer respectively) can significantly increase crop yield, and at the same time, reduce the risk of nitrogen and phosphorus loss from paddy fields effectively. The research results provide a theoretical basis for the prevention and control of non-point source pollution in rice fields of Chaohu Basin.