To understand the output characteristics of non-point source pollution in the irrigation area during the paddy growth period and its impact on the water quality of downstream control sections, a typical paddy irrigation district in southern China was selected as the research object, and a numerical model for simulation of non-point source pollution processes in the field, gully, pond, and control section was constructed based on the SWAT model. The model was used to quantitatively analyze the dynamic response of water quality at the control section under 9 pollution control schemes throughout the entire paddy growth period. The results showed that retreated water and nitrogen and phosphorus pollutants were discharged in a pulsed manner, and the peak of non-point source pollution in paddy field occurred in the first half of paddy growth period, including the transplant regreening stage, tillering stage, and jointing booting stage. Measures of controlled irrigation, ecological engineering, and controlled drainage had good effects on reducing nitrogen and phosphorus pollutants in the first half of paddy growth period, and the reduction effect was significantly improved after the implementation of comprehensive measures, with the reduction rates of TN and TP exceeding 90% during the whole paddy growth period. The effects of single measures on water quality improvement were limited, and fertilization management led to more pulsatile TN mass concentration peaks at the tillering stage. Comprehensive measures could significantly improve the water quality compliance rate, especially, the combined measure of fertilization management, controlled drainage, and ecological engineering and the combined measure of controlled irrigation, fertilization management, controlled drainage, and ecological engineering could ensure the TN and TP mass concentrations to reach the water quality standard.