Natural organic matter (NOM) in the filtrated surface water from a water treatment plant was isolated and fractionated into six types of fractions. These fractions were ozonated at typical ozone dose and reaction time. The yields of several small molecular ozonation by-products, such as, aldehydes, ketones and ketoacids, were monitored after ozonation of the individual NOM fractions. The results showed that formaldehyde and pyruvic acid had the maximal yields among the aldehydes and ketoacids, respectively. Hydrophobic neutral (HON) produced the most significant yield of the ozonation by-products with the specific yield of formaldehyde up to 70.58% of the specific yields and pyruvic acid being 103.2 microg/mg. The hydrophobic NOM fractions produced higher yields of these by-products than the hydrophilic fractions. For example, HON and hydrophobic acid (HOA) produced much higher yields of the ozonation by-products than other fractions. Aldehydes and ketones from HON and HOA and ketoacids from the two fractions accounted for 55.56% and 60% of the ozonation by-products from all the NOM, respectively. Lower production of these by-products was also observed for the basic fractions compared to the acidic and neutral ones. HON and HOA were more biodegradable after ozonation, because their ozonation by-products contributed much higher amount of DOC to the final DOC after ozonation.