Three-dimensional fluorescence spectroscopy (3D-EEMs), infrared spectroscopy, ultraviolet-visible spectroscopy and high-throughput sequencing were used to study the spectral characteristics and microbial diversity during the clogging process of soil infiltration treatment of aged swine wastewater. The experiment was carried out in a pilot scale soil infiltration system. Before the system was completely blocked, DOM was converted to fulvic acid after treatment. When the system was blocked, the composition of DOM remained basically unchanged, but the original protein-like peaks in the influent had a weak red shift, a trend of transformation, and the relative intensity of fluorescence peaks decreased, indicating that the concentration of DOM decreased. The main components of DOM were carbohydrates, phenols, lipids, organic acids and aromatic organic compounds. The occurrence of clogging was beneficial to the removal of colored DOM concentration, and the macromolecular benzene ring structure in the effluent decreases. When the reactor was blocked, the microbial diversity of the lower soil samples was greater than that of the upper soil samples, and the bacterial community diversity was greater than that of the fungi community. Actinobacteria and Alpha haproteobacteria alpha-proteus were the dominant bacteria, and the dominant fungi were Sordariomycetes and Eurotiomycetes.