The quantitative research on pollution loads is the basis of control, evaluation and management of non-point source pollution. The estimation of agricultural non-point source pollution loads includes two steps: evaluation of water discharge and prediction of pollutant concentration in agricultural drain. Water discharge was calculated by DRAINMOD model based on the principle of water balance on farmland. Meanwhile, the synthesis of fertilization and irrigation is used as an impulse input to the farmland, the pollutant concentration changes in agricultural drain is looked as the response process corresponding to the impulse input, the complex migratory and transforming process of pollutant in soil are expressed implied by Inverse Gaussian Probability Density Function. Based on the above, the estimation model of agricultural non-point source pollution loads at field scale was constructed. Taking the typical experimentation area of Qingtongxia Irrigation District in Ningxia as an example, the loads of nitrate nitrogen and total phosphorus in paddy-field drain was simulated by this model. The results show that the simulated accorded with measured data approximately and Nash-Suttcliffe coefficient is 0.963 and 0.945 respectively.