Dissolved organic matter (DOM) has significant influence on the transport and fate of contaminants in multiple phases and it has potential hazard by acting as a precursor of disinfection by-products in water supply. The changes in DOM characteristics, especially by oxidative polymerization might result in different behaviour in the interaction with many contaminants. The aim of this work was to verify the catalytic effects of peroxidase on oxidative polymerization of humic and fulvic substances by examination of the structural characteristics. Transformation of humic acid (HA) and fulvic acid (FA) by oxidative polymerization catalyzed by horseradish peroxidase and hydrogen peroxide were investigated. Size exclusion chromatography, excitation-emission matrices spectra (EEMs), synchronous fluorescence spectra, and infrared spectroscopy was used to evaluate the structural transformation of HA and FA. Molecular weight of HA and FA was continuously changed and their weight-average molecular weight (MWw) reached maximum after 8 h. The MWw of HA and FA were proportionally increased with a dosage of horseradish peroxidase and hydrogen peroxide, indicating that HA and FA was transformed into larger and complex molecules. Spectroscopic results indicated that HA and FA structure contains strong polycyclic aromatic structures with more aromatic rings and a higher degree of conjugation.