Abstract: In order to reduce the losses of nitrogen and phosphorus from paddy fields and to effectively dispose livestock manure, laboratory and field experiments were conducted in the upper Dongjiang river basin, Guangdong Province, China. The field experiments involved five fertilization rations including no fertilizer, conventional urea fertilizer, and three recipe fertilizers. The fertilizers used in these experiments are Ammonium Bicarbonate, Phosphate fertilizer and Organic manure. In respect of Ammonium Bicarbonate, the application rates for these five treatments were 0, 750.0, 510.0, 472.5 and 510.0 kg per hectare; Phosphate fertilizer were 0, 375.0, 255.0, 255.0 and 236.25 kg per hectare; Urea were 0, 225.0, 172.5.0, 156.0 and 172.5 kg per hectare, and 0, 0, 1162.5, 1162.5 and1162.5 kg of Organic manure per hectare were applied for organic manure. Using simulated soil columns indoors, the losses of runoff, nitrogen and phosphorus were obtained for the paddy fields under the condition of no fertilizer. Combined with the laboratory experiment and investigated data from soil samples, water samples, plants, and fertilizer applications in the field, according to the element conservation theory, nitrogen and phosphorus loss models were constructed considering the eluviations, losses and volatilizations of nitrogen and phosphorus as well as their wet and dry sedimentations from the atmosphere. The nitrogen fixation amount in the paddy field was calculated as around 31.54 kg/hm2 during the growth period. The losses of nitrogen and phosphorus were estimated for each of the five treatments, and valuable results were obtained. Compared to the traditional fertilizer application, the three fertilizer rations can decreases in 7.7%-30.0%, 61.2%-70.8% for nitrogen and phosphorus losses, and increases in 24.6%-84.4%, 12.8%-78.9% for their utilization efficiencies. The three fertilizer applications can increase in around 2716 yuan/hm2, -2169 yuan/hm2, and -1646 yuan/hm2, respectively. Among the three fertilizer rations, the first ration one can achieve the high benefit both economically and environmentally, and thus can be considered as a substitute as the conventional urea fertilizer. The study analyzed the input and output of nitrogen, phosphorus in the rice paddy system. Considering the inputs and outputs of nitrogen and phosphorous in the paddy field system, different fertilization rations were evaluated and each fertilization ration were obtained in view of their agronomic efficiency and their ecological and environmental effects. This study would provide rational references using fertilizers in paddy field and control their nitrogen and phosphorus losses in South China.