The species transformation and structure variation of fulvic acid (FA) during ozonation were investigated in this study. The molecular weight (MW) distribution, the species of intermediate products and the variation of polar functional groups were studied by ultrafiltration, gas chromatography/mass spectrometry (GC/MS) and titration analyses respectively. The average MW of FA decreased significantly during ozonation. The amount of polar functional groups (carboxylic and phenolic (ph-OH) groups) per unit DOC (mol/kg C) increased with increasing ozonation time. Furthermore, GC/MS experiments demonstrated the formation of polar species (e.g., hexadecanoic acid, benzoic acid and octadecanoic alcohol) and less-polar species (e.g., aliphatic hydrocarbons and butanedioic acid, bis(2-methylpropyl) ester). Electron spin resonance (ESR) measurements proved the presence of ·OH radicals in the ozonation system. Based on our experimental results, it appears that the oxidations by ozone molecule and ·OH radicals were responsible for the transformation of organics (FA and its oxidation products) during ozonation. These two oxidants showed significant influence on organics transformation and exhibited different mechanisms contributing to these processes.