The prevention and control of agricultural non-point source pollution is an effective way to solve the water ecological environment dilemma in southern China. In this paper, based on the irrigation area scale, three kinds of drainage systems (ditch-sluice gate regulation and storage system (DSG system), field-ditch direct drainage system (FDD system), and ecological ditch-pond regulation and storage system (EDP system) were set up to quantitatively study the purification and removal capacity to reduce nitrogen (N) and phosphorus (P) pollutants. The results showed that the concentration of N and P pollutants in various levels of drainage ditches was generally higher in July, with a significant fluctuation in August and the lowest in September and October. The concentration of N and P pollutants at the inlet of the EDP system was significantly higher, while at the outlet, it was lower than that of the DSG and FDD systems. The removal rates of TN, NO3 --N, NH4 +-N, and TP by the three drainage systems were 14.2~36.2%, 1.9~93.9%, 4.5~15.8%, and 0.4~24.2%, respectively. The EDP system had the highest removal ability of N and P pollutants under the joint action of plants and microorganisms in the drainage ditch. DSG system was equipped with a regulating gate at the end of the farmland ditch, which increased the hydraulic retention time to improve the purification effect of N and P pollutants. The ideal and actual removal rates of pollutants were increased with the increase of pollutant degradation coefficient, while the realization rate showed a flat U-shaped trend with the increase of pollutant degradation coefficient. Integrating farmland and drainage ditches-ponds (wetlands) as a whole could fully utilize the interception and purification effect on pollutants, which would have good feasibility and promotion in practical production.