Abstract: Through the analysis of thet transport of N in the groundwater, ditch and soil profile during the period from the first-autumn irrigation to the second-autumn irrigation in Wulate irrigation region in Hetao Irrigation District Inner Mongolia, and the law of the agricultural non-point pollution production was analyzed so as to provide the corresponding theoretical guidance of the control of nitrogen pollution in Hetao Irrigation District. The study results shows that the accumulation of NO-3-N in the deeper soil profile (120-160 cm) was not significantly during the first-autumn irrigation period. The NO-3-N content were increased by 1.25、2.72 and 2.89 mg/kg in the three farmland soil profiles (80～160 cm) respectively after the second-autumn irrigation period. The NH+4-N distributions were relatively homogeneous from surface to deep of soil profile. The change law of the NO-3-N and NH+4-N content in the three type soil profiles were increased or reduced seasonally. The content of NO-3-N and NH+4-N in the groundwater in the second-autumn irrigation period were higher than that of the first-autumn irrigation period. The second-autumn irrigation period was the key stages which producted the agricultural non-point pollution in Hetao Irrigation District. The NO-3-N and NH+4-N were accumulated in the soil profile of salt wasteland，which was helpful to reduced the amount of the agricultural non-point pollutant discharge.