The manure and domestic sewage of livestock and poultry breeding in the Gun river basin of Zaoyang City are scattered and discharged, and the non-point source pollution are serious. The water quality of the Juwan Control Section was seriously polluted. Using the measured hydrological and water quality data, the water environmental problems of the basin were determined by the calculation of pollution source and water quality status. Based on SWAT model, the non-point source pollution model was constructed, and its parameters were calibrated and validated. The COD and NH3—N loads of the basin and the water qualitative change of the Juwan section were simulated in 2013-2015. The results showed that the COD and NH3—N loads of Zaoyang City in 2015 were 49842.92 t and 6681.08 t, respectively. The study area was dominated by non-point source pollution loads, of which livestock and poultry farming accounted for the largest proportion. The contribution rate of total watershed load was 45.62% and 35.68%, for COD and NH3—N, respectively, followed by urban and rural domestic sewage, and the pollution load of planting industry is low. Therefore, the total amount control measures and load reduction schemes of pollutant discharge in river basins, which were mainly controlled by non-point source pollution, were put forward, and the implementation effects of these schemes were simulated.