Abstract: In order to fully understand the current situation of livestock and poultry farming pollution and its potential impacts on the ecological environment, in the middle route of the South-to-North Water Transfer Project analyse the potential of livestock and poultry manure as a substitute for fertilizers, The environmental risk assessment model of livestock and poultry manure was used to quantitatively analyze the main manure sources structure of each county in 2022 based on the data of 49 county-level livestock and poultry farming quantities and arable land area, and the total nutrient content and organic fertilizer substitution potential of livestock and poultry manure in different regions and species were estimated. The results showed that the total amount of livestock and poultry manure was 1534.02×10⁴ t and the distribution was relatively concentrated. The amount of COD was highest (199.42×10⁴ t), followed by TN (8.6×10⁴ t), and TP production was less (1.77×10⁴ t). 18.37% of the counties in the water source area had potential pollution risk of livestock and poultry breeding, among which Danfeng County was at medium risk, Neixiang County and Maojian districts were risky, Dengzhou, Danjiangkou, Yunyang, Xunyang County, Shanyang County and Wanyuan were at little risk and the rest were at a safe level. The load of animal excretion per hectare of arable land in the water source area was 9.235 t hm^-2, the alarm value was 0.308 and the grade index was I. The total equivalent standard pollution load was 48.165×10¹⁰ m³, and the source structure was obviously inconsistent in different regions. TP was the primary pollutant in livestock and poultry farming, and its equivalent standard pollution load accounts for 36.69% of the total load, followed by TN with the pollution load rate of 35.71%, and the lowest equivalent standard pollution load rate of COD was 27.60%. The pollution of livestock and poultry in the water source area mainly came from pigs and cattle, whose contribution to the total equal pollution load reached 47.90% and 41.77% respectively. The total nutrient resource of manure in the water source was 21.195×10⁴ t, and the theoretical potential of fertilizer substitution was 20.67%. According to the theory of nutrient resource of different livestock and poultry manure, the potential of replacing fertilizer was cattle manure (8.86%) > pig manure (6.50%) > poultry manure (3.05%) > sheep manure (2.26%), the theoretical potential of nitrogen, phosphorus and potassium in animal manure to replace fertilizer was 16.77%, 6.89% and 42.23%, respectively. It was of great significance to control the total livestock and poultry production in potential risk areas, promote structural adjustment in different counties, and realize the resource utilization of livestock and poultry manure instead of fertilizer for promoting green development of the South–North Water Transfer Project aquaculture industry.