Source water samples were collected from Guangzhou segment of Pearl River and filtered through Amicon® YC-05, YM-1, YM-3, YM-10, YM-30, YM-100 and ZM-500 membranes sequentially after pre-treatment. The apparent molecular weights of the 8 fractions were calibrated using high-performance size exclusion chromatograph (HPSEC) and they ranged from 0.36 to 182.6 kDa. These fractionated isolates and the raw water were disinfected by chlorine or chlorine dioxide to determine their disinfection characteristics. Results showed that apparent molecular weight of the main dissolved organic matter (DOM) in the RO isolate of water sample was less than 360 Da and this part of the DOM was mainly from anthropogenic activities and contamination of wastewater. RO fraction was the controlling factor for the raw water disinfection process according to the THMs concentrations detected. Disinfection by chlorine dioxide produced less THMs that by chlorine.