Abstract: Livestock and poultry breeding is one of the most important sources for agricultural non-point source nitrogen pollution. After application of manure fertilizer, the intensity of nitrogen losses through soil erosion and leaching in arable land will increase dramatically. Livestock breeding and manure management is a complicate process including nutrient cycling in animal body and transportation of waste from manure to environment through different routes. Discharge coefficient method was widely used for the evaluation of nitrogen pollution loads from animal breeding. The newest Manure-DNDC model was used for the modelling of biogeochemistry process in animal breeding and manure management, with a case study of Xiaoqinghe watershed in Shandong province. Nitrogen transportation and transfer in animal body, manure and agricultural land, main ways of nitrogen losses as well as spatial and temporal distribution of pollution were analyzed in the paper. The results indicated that nitrogen loss in the process of animal breeding and manure fertilizer application was 46.6 million kg N in Xiaoqinghe watershed in 2008. Nitrogen losses from soil erosion and leaching in arable land caused by manure application were 1 million kg and 5.1 million kg, respectively.