Subsurface drainage system is an efficient system to drain extra flood out from the farmland. But this system also changed the transport pathway and speed of water and the dissolved pollution in farmland. To get a full understanding of vertical transportation of nitrate and phosphate in subsurface drainage agricultural watershed, finite element analysis technology was used to make the numerical simulation of mass transfer of soil column. Results show that there is no water and dissolved pollutant in pipe after 5 h rainfall with intensity of 4 mm/h, because the rainfall in 5 h is not enough to saturate the soil layer from surface to pipe. But if extending the rainfall duration to 10 h, the soil became saturated and then the nitrate and phosphate loss observed. The nitrate loss was extremely higher than phosphate (nitrate concentration is 9-10 mg/L, phosphate is 0.05-0.1 mg/L). After 24 h rainfall event, the nitrate loss reached to the maximum. The nitrate loss in tile water intensity was at an exponential growth but phosphate just increased at a liner growth. This phenomenon may be caused by the differences of material properties.