The vertical distribution characteristics of dissolved organic matter(DOM), which were treated by soil infiltration system with simulated high ammonia nitrogen wastewater, were studied by using three-dimensional excitation emission matrix (3D-EEMs)fluorescence spectroscopy and PARAFAC model. The experiment was carried out on a pilot-scale soil infiltration system with a sampling port at 30 cm intervals from top to bottom. The collected samples were identified with PARAFAC model as having 4 fluorescent components at different points in the system, including two humus substances (C1, C2) and two protein substances (C3, C4) respectively. Correlation analysis showed that there was a significant positive correlation among the four kinds of fluorescence components and most of the physical and chemical indexes. The fluorescence component concentration could indirectly characterize the removal efficiency of nitrogen, phosphorus and other nutrients. The analysis of Fmax showed that tyrosine was the most easily degradable in soil infiltration system, followed by fulvic acid, humic acid and the most difficult to degrade protein.