Abstract: Along highlighted water environmental issues and gradual evolution of point source pollution (PSP) such as industrial waste, agricultural non-point source pollution (AGNSP) due to non-scientific applications of fertilizers and pesticides has had an increasing attention in recent years. On the basis of strengthening field "source control", making the best use of agricultural drainage ditch/pond system (interception process) is critical for agriculture non-point source pollution control and management. Drainage ditches have compound ecosystem structures, which are consisted of water-sediment-plant synergy. Migration and transformation of non-point source solute is important in the study of interception, control and management of agricultural non-point source pollution in drainage ditches. However, non-point source solute transformation processes in each medium in water-sediment-plant system of farmland drainage ditch have remained largely unclear. Based on the analysis of ecological structure and drainage ditch characteristics, this paper described the transformation of non-point source soluble nitrogen in water-sediment-plant system of farmland drainage ditch. In combination with the characteristics of farmland drainage ditch water pollution migration, a model of agricultural water pollution migration in drainage ditch system was constructed. The model was based on continuity equation for flow and pollutants migration. It was used to test, monitor and advance a quantitative method of calculation of the effect of different water-sediment-plant media on attenuation degree of non-point source pollutant in water body. Using Qingshui drainage ditch in the People's Victory Canal Irrigation District in Henan Province as a case study, the model was used to calculate the parameters of a field experimental ditch loaded with ammonia nitrogen and nitrate nitrogen pollutants. The results showed that the simulated and measured values fitted well. The simulation efficiency coefficient of ammonia nitrogen was 0.87 and that of nitrate nitrogen was 0.93. The results demonstrated that the model was available and effective for the simulation of drain pollution in ditches in agricultural farmlands.